Course catalogue for doctoral education VT18kiwas.ki.se/kicoursecatalogueVT18.pdf · 2641 Sickness...

Course catalogue for doctoral education

VT18

# Human biology or pathology * General science courses 1383 Basic Course in Medical Statistics * 20180312 20180323 (English)

1383 Basic Course in Medical Statistics * 20180521 20180601 (English) 1391 Writing science and information literacy * 20180416 20180427 (English)

1447 Introductory course in SAS programming 20180514 20180518 (English) 1551 Cardiovascular Research An overview of the process of atherosclerosis 20180528 20180601 (English)

1561 Health risk assessment: principles and applications 20180312 20180316 (English) 1622 Epidemiology II. Design of epidemiological studies 20180322 20180328 (English) 1684 Epidemiology III. Analysis and interpretation of epidemiological data 20180507 20180515 (English)

1685 Biostatistics III: Survival analysis for epidemiologists * 20180212 20180221 (English) 1873 Quality of life as an outcome measure in care sciences 20180308 20180323 (English) 2001 What is life? The future of biology. 20180130 20180613 (English)

2044 Pathology # 20180514 20180525 (English) 2132 Forskningsetik * 20180123 20180213 (Swedish)

2133 Vetenskapsteori * # 20180227 20180424 (Swedish) 2144 To communicate science in different contexts * 20180206 20180221 (English)

2212 Human embryonic stem cells 20180514 20180518 (English) 2214 Redox regulation, oxidative stress and selenoproteins 20180521 20180525 (English)

2416 Causal Inference for Epidemiological Research 20180226 20180306 (English) 2433 Clinical Research in Lipid Metabolism 20180416 20180420 (English)

2463 Career skills for scientists 20180207 20180315 (English) 2520 Interview techniques in health and care research 20180404 20180503 (English)

2561 Writing science and information literacy * 20180122 20180316 (English) 2609 Basic Course in Medical Statistics a distance course * 20180212 20180223 (English)

2609 Basic Course in Medical Statistics a distance course * 20180507 20180518 (English) 2618 Write your research results and get them published * 20180305 20180316 (English) 2618 Write your research results and get them published * 20180115 20180126 (English) 2618 Write your research results and get them published * 20180416 20180427 (English) 2618 Write your research results and get them published * 20180528 20180608 (English) 2621 Klinisk forskning och Good Clinical Practice: protokoll, informerat samtycke och ansökan i enlighet med

lagar/regler * 20180205 20180209 (Swedish) 2641 Sickness absence research: theories, methods, and concepts 20180205 20180418 (English)

2644 Human physiology an overview # 20180115 20180126 (English) 2666 Methods for statistical analysis: From analysis of variance to multilevel modeling * 20180419 201806

01 (English) 2690 Basic Laboratory Safety * 20180409 20180416 (English)

2690 Basic Laboratory Safety * 20180129 20180205 (English) 2714 Biobanking as a resource for biomedical research 20180312 20180316 (English)

2716 Breast Cancer: Research and treatment 20180514 20180518 (English) 2733 Calcium signaling 20180611 20180615 (English)

2738 Intermediate Medical Statistics: Regression models * 20180409 20180420 (English) 2767 Analysis of genome wide association data 20180308 20180314 (English)

2787 Present your research! * 20180319 20180323 (English) 2787 Present your research! * 20180611 20180615 (English) 2787 Present your research! * 20180205 20180209 (English) 2787 Present your research! * 20180409 20180413 (English) 2787 Present your research! * 20180108 20180112 (English) 2845 Cellbased heart regeneration 20180514 20180518 (English)

2851 Principles of cellular metabolism 20180312 20180323 (English) 2873 Kvalitetssäkring av klinisk forskning * 20180212 20180216 (Swedish)

2873 Quality assurance of clinical research * 20180409 20180413 (English) 2877 Practical approach to animal models in cardiovascular research 20180416 20180420 (English)

2878 Current advances in atherosclerosis research 20180308 20180427 (English) 2879 Principles of toxicology 20180219 20180223 (English)

2888 Regenerative Medicine: Principles to Practice 20180404 20180613 (English) 2896 Core concepts in global health and global burden of disease 20180409 20180413 (English)

2909 Heart failure from pathophysiology to evidence based treatment 20180313 20180320 (English) 2912 Manuscript writing in English * 20180521 20180525 (English)

2928 Public Health Research concepts and theories 20180312 20180323 (English) 2940 Multi modality imaging in oncology 20180305 20180309 (English)

2942 The epigenome: a platform for the integration of metabolic and signaling pathways in development and onthe path to diseases 20180604 20180608 (English)

2948 Principles of nucleic acid structure 20180411 20180427 (English) 2953 Statistics with R from data to publication figure 20180425 20180518 (English)

2957 Neural Control of Inflammation: An introduction to Bioelectronic Medicine 20180611 20180615(English)

2958 Introduction to R 20180528 20180601 (English) 2959 Fundamentals of statistical modeling 20180521 20180525 (English)

2963 Open science and reproducible research 20180305 20180316 (English)

2964 Medical research ethics * 20180212 20180216 (English) 2964 Medical research ethics * 20180514 20180518 (English) 2964 Medicinsk forskningsetik * 20180312 20180316 (Swedish) 2964 Medical research ethics * 20180409 20180413 (English)

2968 Methods for life course epidemiology 20180416 20180420 (English) 2971 Introduction to R data management, analysis and graphical presentation 20180404 20180507

(English) 2996 Anaesthesia, analgesia and surgery (mice and rats) 20180515 20180517 (English)

3022 Translational Paediatric Oncology in the Era of Immunotherapy and Omics 20180423 20180427(English)

3023 Microbiota, metabolism and immunity in the development and treatment of malignancies 20180604 20180608 (English)

3024 Advanced cancer biology 20180109 20180612 (English) 3025 Advanced Cell Culture modelling with human induced pluripotent stem (iPS) cells 20180122 201802

02 (English) 3026 Cell cycle, cancer and anticancer targets 20180319 20180323 (English)

3027 Bioinformatics analysis of gene regulation in omics data and its applications to medical problems * 20180226 20180309 (English)

3028 Grundkurs i SPSS 20180312 20180319 (Swedish) 3029 Observation and visual methods in health care sciences research 20180305 20180425 (English)

3030 Human Papilloma Virus from molecular biology to global health an eLearning course 20180205 20180309 (English)

3031 Introduction to teaching * 20180313 20180412 (English) 3032 Mixed methods: integration of qualitative and quantitative data within applied health research 20180402

20180501 (English) 3035 Imaging in neuroscience: with a focus on MEG and EEG methods 20180205 20180209 (English)

3036 Mouse necropsy 20180411 20180418 (English) 3037 Exploring entrepreneurial opportunities in research 20180226 20180413 (English)

3038 Basic Immunology 20180116 20180308 (English) 3040 Aging Societies: Challenges and Opportunities 20180409 20180427 (English)

3041 Epidemiology I: Introduction to epidemiology 20180307 20180316 (English) 3042 Biostatistics I: Introduction for epidemiologists * 20180404 20180424 (English)

3043 Biostatistics II: Logistic regression for epidemiologists * 20180124 20180131 (English) 3044 Basic bioinformatics * 20180416 20180424 (English)

3045 Computational modelling and data analysis for cognitive neuroscience 20180509 20180525 (English) 3046 Causal inference: emulating a target trial to assess comparative effectiveness 20180319 20180321

(English) 3047 Understanding and fighting disease using structural biology 20180409 20180420 (English)

3049 Cellular Signalling 20180319 20180323 (English)

Title : Basic Course in Medical Statistics

Course number : 1383 Credits : 3.0

Date : 20180312 20180323 Language : English

Level : Doctoral level Responsible KI department : Department of Learning, Informatics, Management and Ethics

Specific entry requirements : Purpose of the course : The aim of the course is to introduce the basic statistical methods and the fundamental

principles of statistical inference and to offer basic skills that involve hands on data analysis using statisticalsoftware.

Learning outcomes : The course participants shall after the course be able to; 1) perform and interpret basicdescriptive statistics from frequency tables and graphical presentations, 2) perform and interpret results from basicinferential statistical analysis and tests, 3) recognize and critically examine the statistics being presented in articleswithin the medical field of research.

Contents of the course : Concepts being treated are descriptive vs inferential statistics, collection of data andstudy design, different types of data and level of measurement, independent and dependent samples, correlationand regression, hypothesis testing and different type of statistical errors in relation to the testing and datacollection procedure. The major topics for the course are ttest, chisquare test, nonparametric test and regressionanalysis, and how to evaluate the assumptions for the different techniques.

Teaching and learning activities : This course is a TeamBased Learning (TBL) course. TBL is a specific form oflearning method that integrates individual assessment and group work with immediate feedback. Focus will be onsolving statistical problems in a team setting. This two weeks course consists of online preparation through videolectures and exercises, and several TBL sessions (in class meeting). The time in between TBL sessions will be spentreading the course material, and preparing for the assessment and group application exercises.

Examination : Individual and group readiness assurance tests, as well as application exercises. Compulsory elements : In class attendance during TBL sessions are mandatory for passing grade. If a student

misses one of the five TBL sessions a supplementary exercise will be given. If the student misses more than oneTBL session it is recommended that the student takes the course at another occasion (since absence also affectsthe other members of the team).

Number of students : 40 45 Selection of students : Date for registration as a doctoral student (priority given to earlier registration date).

Please make sure that you have entered the correct registration date for doctoral education in your personal profile. More information : This course is a TBLcourse. TBL, TeamBased Learning, is a special form of learning that

integrates individual work, group work and immediate feedback. Focus will be on solving statistical problems ingroup/team setting. The course will consist of 23 full days per week for two weeks. Course dates are: March 12,13, 15, 19, 21 and 23.

Course responsible : Mesfin Tessma

Department of Learning, Informatics, Management and Ethics

[email protected]

Contact person : Margareta KrookBrandt

Institutionen för lärande, informatik, management och etik

Margareta.Krook[email protected]

Elisabeth Löfgren Institutionen för lärande, informatik, management och etik

[email protected]

Title : Basic Course in Medical Statistics








Teaching and learning activities : This course is a TeamBased Learning (TBL) course. TBL is a specific form oflearning method that integrates individual assessment and group work with immediate feedback. Focus will be onsolving statistical problems in a team setting. This two weeks course consists of online preparation through videolectures and exercises, and several TBL sessions (in class meeting). The time in between TBL sessions will be spentreading the course material, and preparing for the assessment and group application exercises.

Examination : Individual and group readiness assurance tests, as well as application exercises. Compulsory elements : In class attendance during TBL sessions are mandatory for passing grade. If a student

misses one of the five TBL sessions a supplementary exercise will be given. If the student misses more than oneTBL session it is recommended that the student takes the course at another occasion (since absence also affectsthe other members of the team).

Number of students : 40 45 Selection of students : Selection will be based on 1) the relevance of the course syllabus for the applicant's

doctoral project (according to written motivation), 2) date for registration as a doctoral student (priority given toearlier registration date)

More information : This course is a TBLcourse. TBL, TeamBased Learning, is a special form of learning thatintegrates individual work, group work and immediate feedback. Focus will be on solving statistical problems ingroup/team setting. The course will consist of 23 full days per week for two weeks. Course dates are: May 21, 22,24, 28, 30 and June 1.



[email protected]





[email protected]

Title : Writing science and information literacy



Level : Doctoral level Responsible KI department : Karolinska Institutet University Library

Specific entry requirements : Purpose of the course : The aim of the course is to develop the medical scientific writing skills and information

literacy of the participant. Learning outcomes : After the course, you will be able to demonstrate: understanding of how to write an original

scientific article and submit it for publication. the ability to write other types of texts required for a scientificcareer. the ability to give, take and make use of constructive criticism. the ability to search and manage themedical sciences literature in a structured way. the ability to use resources which facilitate choosing a journal topublish your research. and be able describe aspects of postpublication evaluation and processing of the medicalsciences literature.

Contents of the course : Basics of scientific writing, Searching the literature, Writing an original scientific paper,Supporting the text, Managing the literature, Scientific writing in other contexts, Choosing a journal, Thepublication process, Evaluating published science.

Teaching and learning activities : This is a KI CAMPUS course (there is also an 100% online version with coursecode 2561) with face to face teaching including: individual writing and rewriting, lectures, working in pairs andgroups, webbased teaching, demonstrations, computer exercises and individual study.

Examination : Writing a grant application (including references) with popular science summary and rewritingbased on peer and teacher feedback. There are also three assignments in which participants demonstratedevelopment of their information literacy.

Compulsory elements : The course writing assignment is obligatory and has to be submitted about 10 daysBEFORE course start. All scheduled teaching is compulsory (except where clearly stated otherwise). Absence canusually be compensated for by reading and individual work after consultation with course leaders. There are threeobligatory assignments in relation to information literacy development.



More information :

Course responsible : David Herron

Karolinska Institutet University Library 08524 841 13

[email protected]

Berzelius 7B

17177 Stockholm

Contact person :

Katarina Amcoff Karolinska Institutet universitetsbibliotek

08524 840 47 [email protected]

Title : Introductory course in SAS programming



Level : Doctoral level Responsible KI department : Department of Public Health Sciences

Specific entry requirements : Purpose of the course : The aim is to introduce fundamental SAS programming language for use in database

handling and preparation for analyses. Further, the aim is to introduce the student on how to use statisticalprocedures in SAS, with focus on descriptive statistics.

Learning outcomes : After successfully completing this course you as a student are expected to be able to: apply the SAS system when importing and exporting data. manipulate data using SAS labels and formats. manipulate data using SAS functions and programming statements. perform descriptive statistics using adequateSAS procedures. describe how to use the SAS help manual (SAS OnlineDoc).

Contents of the course : The course is designed to give fundamental insights in the SAS system and basic skillsin the SAS programming language. The course embraces commands for definition, description, modification,selection and analysing of data, and covers: Introduction to the SAS Windows SAS data sets, creating, importingand exporting data Data handling, programming statements and SAS functions SAS procedures for descriptivestatistics

Teaching and learning activities : Fulltime in supervised computer lab with a mixture of interactive lectures andexcercises. Every morning a quiz, recapitulating the previous days' lectures.

Examination : To pass the course, the student has to show that the learning outcomes have been achieved. Thecourse will end with an examination consisting of both an individually written and individually computerized examwhere the covered commands are used. Students who do not obtain a passing grade in the first examination will beoffered a second chance to resubmit the examination within two months of the final day of the course. Studentswho do not obtain a passing grade at the first two examinations will be given top priority for admission the nexttime the course is offered.

Compulsory elements : Only the examination is compulsory. Number of students : 8 20

Selection of students : Eligible doctoral students will be prioritized according to 1) the relevance of the coursesyllabus for the applicant's doctoral project (according to written motivation), 2) date for registration as a doctoralstudent (priority given to earlier registration date). To be considered, submit a completed application form. Give allinformation requested, including a short description of current research training and motivation for attending, aswell as an account of previous courses taken.

More information : The course is held at Karolinska Institutet Campus Solna. Fulltime in supervised computer labwith a mixture of interactive lectures and exercises. Every morning a quiz, recapitulating the previous days'lectures. Basic computer skills are required.

Course responsible : Susanne Wicks

Department of Public Health Sciences 08123 372 01

[email protected]

Contact person : Marita Larsson

Institutionen för folkhälsovetenskap 08524 801 05

[email protected]

Title : Cardiovascular Research An overview of the process ofatherosclerosis



Level : Doctoral level Responsible KI department : Department of Medicine, Solna

Specific entry requirements : Purpose of the course : Atherosclerosis will be discussed from the molecular, cellular, genetic, clinical and

epidemiological viewpoints. Therefore, participants with a medical background will have the possibility to be moreexposed to experimental work and, conversely, participants with a nonmedical background will be enabled toobtain good knowledge of distinct clinical manifestations of atherosclerosis. This will be useful for, among others,bioinformaticians in the field. In addition, the course gives the participants the possibility to network with otherstudents in the cardiovascular field.

Learning outcomes : The participant should be able to: 1. Relate risk factors with the pathology ofatherosclerosis 2. Discuss the development of the atherosclerotic lesion on cellular and molecular level 3. Motivatethe use of different models (in vitro, epidemiological, animal model) to study atherosclerosis and apply them to agiven project.

Contents of the course : Atherosclerosis will be discussed from the molecular, cellular, genetic, clinical andepidemiological viewpoints. Topics to be covered include discussions of the roles of the following in atherosclerosis:lipids and lipoproteins; oxLDL; thrombosis; plaque stability; inflammation; innate and adaptive immunity;proteinases; blood pressure; and diabetes/insulin resistance. Examples of in vitro and animal models as well asclinical studies will be discussed.

Teaching and learning activities : Lectures, project group, presentation by participants. Examination : To pass the course, the participant has to: 1) Give a presentation in a seminar and to be able to

discuss the different aspects of atherosclerosis with the course leader and the other participants. 2) To be able todiscuss the other participants' presentations. 3) Pass a written exam recapitulating the course's content.

Compulsory elements : Examination is compulsory to pass the course. Number of students : 15 25

Selection of students : Selection will be based on: 1) field of study (priority given to cardiovascular, metabolicand chronic inflammatory disease fields), 2) date for registration as a doctoral student (priority given to earlierregistration date), 3) expressed written motivation to attend the course.

More information : Course location: CMM KI Hospital Solna (http://cmm.ki.se/) Time: 09:00 16:00 all days

Course responsible : Daniel Ketelhuth

Department of Medicine, Solna

[email protected]

Contact person : Angela Silveira

Institutionen för medicin, Solna 0851773224

[email protected]

Title : Health risk assessment: principles and applications



Level : Doctoral level Responsible KI department : The institute of Environmental Medicine

Specific entry requirements : Purpose of the course : The purpose of this course is to build knowledge and understanding of the scientific

method to assess risks to humans of exposure to different types of chemicals. Learning outcomes : Upon completion of the course, the student should be able to: describe the basic concepts

and principles of health risk assessment of chemical substances explain how different types of data from invivo/animal, epidemiological and in vitro studies as well as exposure data are used in risk assessment assess therelevance and reliability of data used in risk assessment derive health based guidance values such as AcceptableDaily Intake (ADI) based on the data reflect on the role of health risk assessment in regulatory decision making

Contents of the course : Health risk assessment of chemicals is the scientific method to assess the risk tohumans of exposure to different types of chemical substances, such as pharmaceuticals, environmental pollutants,chemicals in cosmetics, clothing or other everyday products and pesticide residues, food additives and othersubstances in food. The course starts off with introducing the concepts in risk assessment, e.g. aims of riskassessment, role of risk assessment in risk analysis (risk assessment, risk management, risk communication),different steps in risk assessment (hazard identification, hazard characterisation, exposure assessment, riskcharacterisation). It moves on to the different types of data from in vivo/animal, epidemiological and in vitrostudies as well as exposure data that are used in risk assessment. Thereafter it is discussed how the relevance andreliability of the data is assessed, and how different types of evidence are integrated (for example from animal andepidemiological studies). The principles on how to derive healthbased guidance values such as Acceptable DailyIntake (ADI) and to derive Margins of Safety values based on the data are exercised. The course then moves on toprovide examples of the role of risk assessment in regulatory decision making. Case studies of different types ofrisk assessments exemplify how research connects to risk assessment activities. The participants will also discusshow their own research can contribute to risk assessments.

Teaching and learning activities : Teaching and learning activities include lectures, exercises and groupassignments.

Examination : Examination is in the form of a written assignment and/or oral presentation. Compulsory elements : Participation in the exercises and group assignments is compulsory. Absence can be

compensated with an individual task. Number of students : 8 30

Selection of students : Selection will be based on 1) the relevance of the course syllabus for the applicant'sdoctoral project (according to written motivation), 2) date for registration as a doctoral student (priority given toearlier registration date)

More information :

Course responsible : Anna Beronius

The institute of Environmental Medicine

[email protected]

Contact person : Johanna Bergman Institutet för miljömedicin

[email protected]

Nobels väg 13

17177

Stockholm

Title : Epidemiology II. Design of epidemiological studies




Specific entry requirements : Knowledge in epidemiology equivalent to "Epidemiology I: Introduction toepidemiology" or corresponding courses.

Purpose of the course : The course focuses on key considerations in designing and critically interpreting differenttypes of casecontrol studies, as well as matching in cohort and casecontrol studies.

Learning outcomes : After successfully completing this course you as a student are expected to be able to: in aselfdirected manner, formulate the principles of different types of common epidemiological study designs. mainlyindependently, explain how a specific measure of disease occurrence and measure of association is governed by thestudy design. in a selfdirected manner, explain and discuss epidemiological concepts, including accuracy, in thecontext of different epidemiological study designs. draw conclusions from epidemiological scientific papers and toreview and criticize these regarding study design, results and accuracy. Learning outcomes are classifiedaccording to Bloom's taxonomy: knowledge, comprehension, application, analysis, synthesis, and evaluation.

Contents of the course : The course focuses on issues related to study design with emphasis on casecontrolmethodology and different types of sampling strategies, study base, study efficiency, matching in epidemiologicalstudies, induction time, interpretation of epidemiological evidence.

Teaching and learning activities : Lectures, group discussions and various forms of group exercises on selectedtopics, will be used. The course focuses on active learning, i.e. putting knowledge into practice and criticallyreflecting upon the knowledge, rather than memorising facts.

Examination : To pass the course, the student has to show that the learning outcomes have been achieved.Assessments methods used are group tasks (formative assessments) along with a written individual task(summative assessment).The examination is viewed as a contributing to the development of knowledge, ratherthan as a test of knowledge. Students who do not obtain a passing grade in the first examination will be offered asecond examination within two months of the final day of the course. Students who do not obtain a passing gradeat the first two examinations will be given top priority for admission the next time the course is offered. Compulsory elements : The individual examination .

Number of students : 8 25 Selection of students : Eligible doctoral students, with required prerequisite knowledge, prioritized according to

1) the relevance of the course syllabus for the applicant's doctoral project (according to written motivation), 2) datefor registration as a doctoral student (priority given to earlier registration date). To be considered, submit acompleted application form. Give all information requested, including a description of current research andmotivation for attending, and an account of previous courses taken.

More information : Course dates are March 22, 23, 26, 27 and 28. The course is extended over time, but is still 5full course days in order to promote reflection and reinforce learning. The individual examination will be performedas a takehome examination.

Course responsible : Karin Leander

The institute of Environmental Medicine 0852487498

[email protected]

Box 210 (Nobels väg 13), KI

171 77 Stockholm

Contact person :

Johanna Bergman Institutet för miljömedicin

[email protected]

Nobels väg 13

17177

Stockholm

Title : Epidemiology III. Analysis and interpretation ofepidemiological data




Specific entry requirements : Knowledge equivalent to "Epidemiology I: Introduction to epidemiology","Epidemiology II: Design of epidemiological studies", "Biostatistics I: Introduction for epidemiologists" orcorresponding courses.

Purpose of the course : The purpose of the course is to familiarise the student with principles for epidemiologicaldata analysis and critical interpretation of study results.

Learning outcomes : After successfully completing this course you as a student are expected to be able to: analyse and interpret measures of association between exposure and disease in different study designs, analyseand interpret interactions between causes, reason about principles of causal inference, evaluate methodologicalaspects when critically reviewing individual epidemiological studies, apply good practices for quantitative biasanalysis to epidemiological data, and demonstrate how to communicate areas of expertise to the public and tothose not familiar with your research area.

Contents of the course : The course focuses on issues related to causal inference, principles of epidemiologicaldata analysis, and interpretation of epidemiological concepts and principles of relevance when critically reviewingindividual epidemiological studies.

Teaching and learning activities : Lectures, group discussions and various forms of group exercises on selectedtopics, will be used. The course focuses on active learning, i.e. putting knowledge into practice and criticallyreflecting upon the knowledge, rather than memorising facts.

Examination : To pass the course, the student has to show that all the intended learning outcomes have beenachieved. Assessments methods used are group assignments (formative assessments) along with a writtenindividual takehome examination. The examination is viewed as contributing to the development of knowledge,rather than as a test of knowledge. Students who do not obtain a passing grade in the first examination will beoffered a second chance to resubmit the examination within two months of the final day of the course. Studentswho do not obtain a passing grade at the first two examinations will be given top priority for admission the nexttime the course is offered.

Compulsory elements : Individual examination task (summative assessment). Number of students : 8 25

Selection of students : Eligible doctoral students, with required prerequisite knowledge, prioritized according to1) the relevance of the course syllabus for the applicant's doctoral project (according to written motivation), 2) datefor registration as a doctoral student (priority given to earlier registration date). To be considered, submit acompleted application form. Give all information requested, including a description of current research andmotivation for attending, and an account of previous courses taken.

More information : Course dates are May 7, 8, 9, 14 and 15. The individual examination will be performed as atakehome examination, and will be distributed the last day of the course.

Course responsible : Lars Alfredsson


[email protected]


[email protected]

Nobels väg 13

17177

Stockholm

Title : Biostatistics III: Survival analysis for epidemiologists



Level : Doctoral level Responsible KI department : Department of Medical Epidemiology and Biostatistics

Specific entry requirements : Epidemiology I: Introduction to epidemiology, Biostatistics I: Introduction forepidemiologists and Biostatistics II: Logistic regression for epidemiologists or equivalent courses, and practicalexperience applying statistical models.

Purpose of the course : This course focuses on the application of survival analysis methods to epidemiologicalstudies. The statistical software Stata will be used in the course.

Learning outcomes : After successfully completing this course students should be able to: propose a suitablestatistical model for assessing a specific research hypothesis using data from a cohort study, fit the model usingstandard statistical software, evaluate the fit of the model, and interpret the results. explain the similarities anddifferences between Cox regression and Poisson regression. discuss the concept of timescales in statisticalmodels for timetoevent data, control for different timescales using standard statistical software, and argue for anappropriate timescale for a given research hypothesis. discuss the concept of confounding in epidemiologicalstudies and control/adjust for confounding using statistical models. apply and interpret appropriate statisticalmodels for studying effect modification and be able to reparameterise a statistical model to estimate appropriatecontrasts. critically evaluate the methodological aspects (design and analysis) of a scientific article reporting acohort study.

Contents of the course : This course introduces statistical methods for survival analysis with emphasis on theapplication of such methods to the analysis of epidemiological cohort studies. Topics covered include methods forestimating survival (life table and KaplanMeier methods), comparing survival between subgroups (logrank test),and modelling survival (primarily Poisson regression and the Cox proportional hazards model). The courseaddresses the concept of 'time' as a potential confounder or effect modifier and approaches to defining 'time' (e.g.,time since entry, attained age, calendar time). The course will emphasise the basic concepts of statistical modellingin epidemiology, such as controlling for confounding and assessing effect modification.

Teaching and learning activities : Lectures, exercises focusing on analysis of real data using statistical software,exercises not requiring statistical software, group discussions, literature review.

Examination : The course grade is based solely on a written examination. The examination will contain twosections and a passing grade must be obtained for each section in order to obtain a passing grade for the course.Students who do not obtain a passing grade on both sections and wish to take the examination again must retakethe entire examination (i.e., both sections) even if they previously obtained a passing grade on one of the twosections. The focus of the exam will be on understanding concepts and their application to analysis ofepidemiological studies rather than mathematical detail. Students who do not obtain a passing grade in the firstexamination will be offered a second examination within 2 months of the final day of the course. Students who donot obtain a passing grade at the first two examinations will be given top priority for admission the next time thecourse is offered. If the course is not offered during the following two academic terms then a third examination willbe scheduled within 12 months of the final day of the course.

Compulsory elements : The individual examination (summative assessment). Number of students : 8 25

Selection of students : Highest priority will be given to applicants previously enrolled in the course withoutobtaining a passing grade. Other eligible applicants with appropriate prerequisite knowledge will be prioritizedaccording to the relevance of the course for their research training. Please provide a short description of currentresearch training and motivation for attending the course, along with a description of relevant previous coursestaken.

More information : The course will be held February 12, 14, 16, 19, 21. The course is extended over two weeks(but still five course days) to promote reflection and active learning. Participants are expected to have prerequisiteknowledge equivalent to the learning outcomes of the courses Epidemiology I, Biostatistics I and Biostatistics II. We have provided a selfassessment test (http://biostat3.net/download/selfassessment.pdf) for you toconfirm that you understand the central concepts. We advise all potential applicants to take the test prior toapplying for Biostatistics III. If you attempt the test under examination conditions (i.e., without referring to theanswers), we would recommend: 1. if you score 70% or more then you possess the required prerequisiteknowledge; 2. if you score 40% to 70% you should revise the areas where you lost marks; 3. if youscore less than 40% you should, at a minimum, undertake an extensive review of central concepts in statisticalmodelling and possibly consider studying intermediatelevel courses (e.g., Biostatistics II) before takingBiostatistics III. The statistical software Stata will be used throughout the course. Participants are expectedto possess basic knowledge of Stata prior to the start of the course. An introduction to Stata can be downloadedfrom the course webpage (www.biostat3.net).

Course responsible : Mark Clements

Department of Medical Epidemiology and Biostatistics

[email protected]

Contact person : Gunilla Nilsson Roos Institutionen för medicinsk epidemiologi och biostatistik


Title : Quality of life as an outcome measure in care sciences



Level : Doctoral level Responsible KI department : Department of Neurobiology, Care Sciences and Society

Specific entry requirements : Purpose of the course : The course aims to give doctoral students a basic understanding of the theory behind

measurement of quality of life and introduce the methods used when conducting studies with quality of life as anoutcome measure. Students will get the opportunity to dig into their own research by critically reviewing theinstruments they are using and to orally defend the methods they are using.

Learning outcomes : After the course, the students should be able to critically review research papers analyzingquality of life. This includes phrasing research questions, choosing appropriate instruments, timing of assessmentsand procedure as well as choosing methods for analysis. Furthermore should students be able to interpret anddiscuss results from studies of quality of life.

Contents of the course : The concept quality of life and healthrelated quality of life will be discussed to giveinsights into these concepts. Aditionally the criticism against these concepts and their measurement will beaddressed.The course will further include phrasing research questions, choosing appropirate instruments, designingstudies measuring quality of life (timing of assessments and procedure), choice of methods for analysis, andinterpretation of results.

Teaching and learning activities : Learning activities include lectures, groupseminars and assignments. Examination : Doctoral students are required to accomplish a number of assignments which will be presented thefirst day of the course. Assignments are typically prepared and worked through at home and thereafter followed upand discussed in class.

Compulsory elements : Assignments and seminars are compulsory. Absence from groupseminars will be madeup with essaywriting on the topics that were to be discussed during the seminar.



More information : Course activities are scheduled to 89 and 2123 of March.

Course responsible : Lena Wettergren

Department of Neurobiology, Care Sciences and Society 0852483650

[email protected]

Contact person : Lars Eriksson

Institutionen för lärande, informatik, management och etik 08 524 83831

[email protected]

Title : What is life? The future of biology.



Level : Doctoral level Responsible KI department : Department of Microbiology, Tumor and Cell Biologi

Specific entry requirements : Purpose of the course : This course should be chosen by those curious of where biomedicine will take us next.

What are the possibilities and challenges with new high through put technologies? How accessible to research arecomplex systems like cells, organisms or brains? The students will also acquire an understanding of the conceptualand technical challenges in future biomedicine and advance their ability to ask scientific questions and identifysignificant and possible areas for problem solving. You will be involved in advanced reasoning on issues at theborderline of knowledge .

Learning outcomes : After the course students shall be able to discuss: 1. Theories about complexity of biologicalsystems 2. How biocomplexity can be studied. 3. The role of computational simulations in modern biology. Howsimulations can be done and what the predictive power is. How mathematics can be used in simulating biologicalphenomena. 4. How one understands the organisational principles of biological systems. If selforganisation is afield for study or just a trivial phenomenon. 5. How evolutionary theory can be formalised into mathematicalmodels. 6. If quantum mechanical theory can have a role in molecular biology. 7. How genetic information can beconverted to mechanical or electrical force in biological system.

Contents of the course : Inspired by the seminal book by Erwin Schrödinger "What is life?" published close to 75years ago we will adress this question again, in view of the impressive development since then. There are manynew concepts to consider in the future of biology, such as the consequencies of the omics era, complexity,computation and simulation, as well as the role of mathematicss and physics in biological theory. The course willcover areas such as biocomplexity, quantum mechanical theory in biology, computation and simulation (in silicobiology), organization of biological systems, causality in biology, how does chemistry become electric and magneticforces and evolutionary theory in the light of molecular biology. Leading scientists with an overview perspective willbe invited to discuss in the seminar form the challenges that meet us today in biology, as a result of the omicsera, the availability of large amounts of data as a result of high throughput techniques, and the possibilitiesprovided by mathematics, simulation theory and computational biology. Young scientists in this areas are alsoinvited to lecture from their perspective.

Teaching and learning activities : Onetwo seminars + workshops every month for five months. Every occasionconsists of a 12 hour seminar with the invited expert, followed by a two hour workshop of basic concepts, i. e. 34hours on each occassion. For each seminar the students will usually be given one article on the topic to read. Active participation in discussions in groups with invited speaker of high international standards is a key element.Some lectures are shown as recorded DVDlectures. You also receive DVDrecordings of all lectures for further selfstudies at home.

Examination : Formatively during the workshop discussions. Summatively by a written individual homeexam(essay) covering the intended learning outcomes of the course.

Compulsory elements : The seminars and workshops are compulsory. Absence has to be compensated by anextra assignment after discussion with the course leader.



More information : Every occassion with a lecture consists of appr 60 min lecture, followed by 1,5 hrs discussionin a smaller group, 12 lectures/month at 3 pm. They take place in the Wallenberg lecture Hall at Nobel Forum orother lecture hall at KI Solna Campus, The lecturers invited are Swedish or International high class speakers withtopis intreresting to the What is lifetheme. We have had guests speakers earlier such as Jim Watson, Craig Venter,Sydney Brenner or Antjé Jacklén. Occassionally instead a "live" speaker we show recordings of some earlierlectures. All lectures are recorded on DVD/YouTube and made available to all the partcipants. This termSchrödingers book "What is life?" will be included as course litterature as well as Chapters from Ernberg I, What islife? (eng translation of Vad är liv? Ernberg et al 2010, KI Univ Press)

Course responsible : Ingemar Ernberg

Department of Microbiology, Tumor and Cell Biologi +46852486262

[email protected]

Box 280, Karolinska Institutet

17177 Stockholm

Contact person :

Title : Pathology



Level : Doctoral level Responsible KI department : Department of Laboratory Medicine

Specific entry requirements : Purpose of the course : The aim of the course is to enable doctoral students lacking basic higher education

knowledge in medicine to understand basic pathological events, such as tissue injury, repair and inflammation andtheir relation to the development of diseases, and how these alterations are coupled to the microstructure ofpathological tissues.

Learning outcomes : After the course the student should 1) understand the mechanisms behind basicpathological events; 2) be able to identify selected pathological tissues at light microscopical level and describe thecomponents/cells and their functions; 3) be able to search for and combine information regarding a selected groupof diseases, followed by an oral presentation and discussion.

Contents of the course : The course is divided into two parts. One part illustrates cell injury, adaptation, tissuerepair and inflammation. Methods in cellular and molecular pathology are discussed. During the other part of thecourse a selected group of diseases are studied both during microscopy practices and as a written and an oralpresentation. How basic pathological responses to inflammation or injury might be the first steps on a multisteppath to malignancy is also discussed.

Teaching and learning activities : This is a full time course with lectures, demonstrations, microscopy exercisesand a project work.

Examination : Written examination and project work. Compulsory elements : Demonstration/microscopy, pathology "tour" and project work are compulsory. Absence

is compensated with a written report. Number of students : 16 30

Selection of students : Selection will be based on 1) documented knowledge in areas such as human tissuebiology, cell biology or physiology (this kind of knowledge is a prerequisite to be able to benefit from the course).Those who already have studied pathology earlier (for example medical doctors) are not prioritized. 2) Date ofadmission to doctoral studies (those who have been admitted longest time ago have priority).

More information :

Course responsible : Barbro EkRylander

Department of Laboratory Medicine 0858586444

Barbro.Ek[email protected]

Contact person : Pia Laselle

Institutionen för laboratoriemedicin

[email protected]

Barbro EkRylander Institutionen för laboratoriemedicin

0858586444 Barbro.Ek[email protected]

Title : Forskningsetik


Date : 20180123 20180213 Language : Swedish

Level : Forskarnivå Responsible KI department : Department for Clinical Science, Intervention and Technology

Specific entry requirements : Purpose of the course : Få en inblick i och förståelse av centrala forskningsetiska teorier, principer och riktlinjer

och därmed få möjlighet att reflektera över etiska aspekter av den egna och andras forskning. Learning outcomes : Den forskarstuderande ska efter att ha gått kursen kunna: 1. Redogöra för forskningsetiska

teorier, principer och till viss del riktlinjer, 2. Visa kunskap angående vanliga forskningsetiska problemsituationeroch de etiska verktygen som kan användas för att hantera forskningsetiska konflikter Färdigheter: Denforskarstuderande ska efter att ha gått kursen kunna: 1. Analysera forskningsetiska konflikter, 2. Ge hållbaraforskningsetiska argument för eller mot ett förfarande Förhållningssätt: Den forskarstuderande ska efter att hagått kursen ha: 1. Utvecklat ett forskningsetiskt förhållningssätt till andra forskarstuderande, handledare ochseniora forskare, 2. Förståelse för hur ett etiskt förhållningsätt uppfattas hos allmänheten 3. Förståelse för vilkenroll forskarens egen hederlighet och integritet har

Contents of the course : Att ge en introduktion till etiken i samband med forskning och en orientering om desstillämpning på problem inom det vetenskapliga området. Kursen behandlar bl.a. följande teman: centrala etiskaprinciper, teorier och argument, forskningsetik/forskaretik, grundläggande värderingar och normer för god sed iforskningen, innehåll i och värdet av regelverk så som Helsingforsdeklarationen dess funktion, tillämpning,möjligheter och begränsningar, etikprövningar, avvikelser från värderingar, forskningsfusk och vetenskapligoredlighet. Det informerade samtyckets historia och komponenter. Försöksdjursetisk, innefattande argument föroch emot att använda olika djur för forskningsändamål samt de 3 R:en. Hantering av vetenskapligt författarskap(medförfattarskap, författarordning) och intressekonflikter i forskningen.

Teaching and learning activities : Föreläsningar (ca 6t), gruppövningar, seminarier(ca 8t) och muntlig ochskriftlig presentation

Examination : Vi bedömer att lärandemålen för kursen är uppnådda genom examination som består av fyradelkomponenter: i) formativ och summativ bedömning i samband med aktivt deltagande i seminarier, ii) enmuntlig presentation av etiska dilemman i egen eller aktuellt forskningsområde, iii) ett skriftligt PM där synpunkterfrån opponent på den muntliga presentationen inarbetats, och iv) opponering på annan students presentation avetiska dilemman i forskning. Godkänd kurs innebär att det framgår att erforderliga kunskaper, färdigheter ochförhållningssätt har uppnåtts genom aktivt deltagande i seminarier och godkänd muntlig och skriftlig presentationav examinationsuppgiften samt opponering på annan students presentation av etiskt dilemma.

Compulsory elements : Obligatoriskt är att delta vid introduktionstillfället och vid seminarier. Vid frånvaro kandetta kompenseras med utökat PM skrivande och muntlig presentation för kursen eller kursgivare.

Number of students : 15 20 Selection of students : Urvalet baseras på 1) kursplanens relevans för den sökandes doktorandprojekt (enligt

motivering), 2) datum för doktorandregistrering (där tidigare registreringsdatum har förtur) More information : Kursen ges en eftermiddag per vecka (tisdagar kl.13:3017:15) under totalt fyra veckor på

Karolinska Universitetssjukhuset, Huddinge (B31/K32). Kursen innehåller föreläsningar, seminarier, gruppövningarsamt studenters muntliga och skriftliga presentationer. Mellan kurstillfällena finns det material att läsa enligt ettschema som ges till de antagna.

Course responsible : Sigridur Kalman

Department for Clinical Science, Intervention and Technology 08585 817 87

[email protected]

Contact person : Isabel ClimentJohansson

Institutionen för klinisk vetenskap, intervention och teknik

isabel.climent[email protected]

Title : Vetenskapsteori



Level : Forskarnivå Responsible KI department : Department for Clinical Science, Intervention and Technology

Specific entry requirements : Purpose of the course : Få en kunskap om, färdighet i och förståelse för grundläggande vetenskapsteoretiska

teorier, principer och diskurser som bildar basen för vetenskaplig metod och kritik. Learning outcomes : Efter kursen skall doktoranden ha kunskaper om 1. Vetenskapsteoretiska teorier, principer

och grundläggande begrepp 2. Aktuella diskurser om vad som är vetenskaplighet Efter kursen skall doktorandenha färdigheter i att 1. Analysera och beskriva forskning i vetenskapsteoretiska termer 2. Delta ivetenskapsteoretisk diskurs om forskning och argumentera för styrkor och svagheter med olikavetenskapsteoretiska ingångar till en frågeställning Efter kursen skall doktorandens förhållningssätt tillvetenskaplig diskurs vara 1. Grundad i respekt för den roll som dialogen och debatten har i utvecklandet avvetenskap 2. Byggd på insikt av att vetenskaplig diskurs kräver respektfull attityd till andra forskare,forskningsområden och samhälle

Contents of the course : En introduktion till vetenskapsteorin och en förståelse för olika slag av vetenskapligtkunskapssökande. En grundläggande orientering om vetenskapsteoretiska frågor ges. Följande teman behandlas:begreppet kunskap, vetenskap pseudovetenskap, hypoteser hypotesprövning, orsaker förklaringar,vetenskapliga värderingar samhälle.

Teaching and learning activities : Föreläsningar (ca 12 t), gruppövningar, seminarier (ca 14 t) och muntlig ochskriftlig presentation.

Examination : Vi bedömer att lärandemålen för kursen är uppnådda genom examination som består av fyradelkomponenter: i) formativ och summativ bedömning i samband med aktivt deltagande i seminarier ii) en muntligpresentation av vetenskapsteoretiska aspekter i eget alternativt andra (centrala) forskningsfrågor inom den egnadisciplinen iii) ett skriftligt PM där synpunkter från opponent på den muntliga presentationen inarbetats iv)opponering på annan students presentation av vetenskapsteoretiska aspekter i egen eller alternativt andra(centrala) forskningsfrågor inom den egna disciplinen Godkänd kurs innebär att det framgår att de erforderligakunskaper, färdigheter och förhållningssätt har uppnåtts genom aktivt deltagande i seminarier och godkänd muntligoch skriftlig presentation av examinationsuppgiften samt opponering på annan students presentation av etisktdilemma.

Compulsory elements : Obligatoriskt är att delta vid introduktionstillfället och vid seminarier. Vid frånvaro kandetta kompenseras med utökad PM skrivande muntlig och presentation för kursen eller för kursgivaren.


motivering), 2) datum för doktorandregistrering (där tidigare registreringsdatum har förtur) More information : Kursen ges en eftermiddag per vecka (tisdagar ca kl.13:3017:15) under totalt nio veckor på

Karolinska Universitetssjukhuset, Huddinge (B31/K32). Kursen innehåller föreläsningar, seminarier, gruppövningarsamt studenters muntliga och skriftliga presentationer. Flera föreläsningar ges av externa föreläsare. Mellankurstillfällena finns det material att läsa och presentationer att förbereda enligt ett schema som ges till de antagna.

Course responsible : Sigridur Kalman

Department for Clinical Science, Intervention and Technology 08585 817 87

[email protected]

Contact person : Isabel ClimentJohansson


isabel.climent[email protected]

Title : To communicate science in different contexts




Specific entry requirements : Purpose of the course : The course aims are orally presentation of own research adapted to different groups and

reflection on presentation skills and ability. Learning outcomes : After the course the student is expected to be able to: 1. Orally present own research

adapted to different target groups. 2. Reflect on presentation skills and ability to adapt to different target groups. Contents of the course : During the course each participant will be given the opportunity to develop practical and

theoretical knowledge in: Communication, perception and learning Presentation techniques Rhetoric Use ofdifferent media (such as Posters, Overheadprojector, PowerPoint, Whiteboard)

Teaching and learning activities : The course design is based on reflective practice and includes selfdirectedlearning, lectures and literature seminar to process theoretical knowledge, and practical training in presentationskills. Each course participant will perform three oral presentations and receive feedback on content, presentationskills and adaptation towards target group.

Examination : The assessment consists of two different tasks: 1. Reflective statement based in experience,feedback and research/literature within communication and learning. 1. Oral presentation in a popular scientificcontext supported by PowerPoint or similar. To pass the course the participant needs to show evidence that theyreached the learning outcomes by fulfillment of the assessment criteria.

Compulsory elements : Compulsory sessions are: 1. Oral presentation in a popular science context (videorecorded) 2. Oral presentation in a scientific context and observe and give feedback to an oral presentation madeby a peer. Absence from the compulsory sessions or assessment seminar can be compensated throughsupplementary activity.

Number of students : 20 30 Selection of students : The selection for this basic general science course will be based on your admission date to

doctoral education (priority given to earlier registration date). Please make sure that you have entered the correctregistration date for doctoral education in your personal profile.

More information : This is a twoweek course which requires time for independent work outside of scheduledclass time. Scheduled class room sessions are on the following dates: 67 February, 1314 February and 2021February. The course is given in ENGLISH.

Course responsible : Cormac Mcgrath


[email protected]




Title : Human embryonic stem cells



Level : Doctoral level Responsible KI department : Department of Biosciences and Nutrition

Specific entry requirements : Purpose of the course : The purpose of the course is to enable doctoral students to obtain a basic understanding

of human reproductive biology with focus on human embryonic stem cell knowledge and cells replacementtherapies and translational medicine. Experts in the field will provide a fresh overview of clinical and preclinicalresearch aiming at development of novel treatment possibilities, but also discussing current limitations and generalethical aspects. Finally the students will be enabled to improve their capacity to produce coherent, logical andconcise explanations of data and concepts both written and orally, through consideration of the course material.

Learning outcomes : At the conclusion of this course students should be able to show a comprehensive view of: Pre implantation Embryology Derivation methods and culture conditions of hESCs Nutritional requirements ofthe blastocyst and stem cells Functional characteristics of different tissue culture incubators Characterization ofthe embryonic stem cells and the importance of the pluripotency of these cells and what is ongoing in this field Production of isogenics embryonic stem cells by somatic cell nuclear transfer (SCNT) The pluripotence induction ofsomatic cell by transduction (the iPS cells) Know the prospective possibilities of having a good culture system andbe aware of potential development of hESC technology in the future. Be aware of the general aspects andimplication of the stem cells research and the potentiality that these represent for clinical application.

Contents of the course : 1. Embryology theory (lectures) 2. In vitro culture system (lectures) 3. HumanEmbryonic Stem cells culture (lectures) 4. Characterization of hESC (lectures) 5. Laboratory demonstrations 6.Genetics (lectures) 7. Introduction to different cell types (lectures) 8. Cell reprogramming (lectures) 9. Stem cellstherapy and challenge today 10. Future in human embryonic stem cells (lecture) Course test, evaluation,discussions, examination and closing of course.

Teaching and learning activities : Lectures and laboratory demonstrations. Examination : Written individual examination

Compulsory elements : The laboratory parts are obligatory. If absent at laboratory activity; student shouldpresent a literature work related with the subject of the missing activity



More information : The course will be held at Karolinska Institutet, Department of Biosciences and Nutrition,Novum Huddinge.

Course responsible : Jose Inzunza

Department of Biosciences and Nutrition 08585 850 93

[email protected]

Hälsovägen 7, Novum

141 86 Stockholm

Contact person :

Jose Inzunza Institutionen för biovetenskaper och näringslära


Hälsovägen 7, Novum

141 86

Stockholm

Title : Redox regulation, oxidative stress and selenoproteins



Level : Doctoral level Responsible KI department : Department of Medical Biochemistry and Biophysics

Specific entry requirements : Purpose of the course : The purpose of the course is to give doctoral students and post docs a good

understanding of redox biology and redox biochemistry in living cells and organisms. The course is also designed togive the participants experience in scientific networking, and to increase generic skills in understanding, presentingand discussing frontline research topics.

Learning outcomes : After the course, each student should have acquired the following knowledge: Goodknowledge of structurefunction relationships for the major low molecularweight antioxidant compounds found incells (GSH, Ascorbate, tocopherol) Good knowledge of the major antioxidant and redox regulatory systems andredox sensitive signaling pathways (glutathionedependent systems, thioredoxin systems, Nrf2/Keap1, Yap1,peroxiredoxins, methionine sulfoxide reductases, peroxidases, catalases, superoxide dismutase, NADPHoxidase,oxidative burst, PTP regulation, cyt c, ASK1) Good knowledge of selenoprotein synthesis and selenoproteinfunction After the course, each student should also have the skill to present and discuss a redoxregulatedresearch project at a level generally expected for presentations held at international cuttingedge conferences inthe subject.

Contents of the course : The course is planned as a joint training encompassing an international exchangegraduate course, with students and lecturer's primarily recruited from Karolinska Institutet together with MedicalUniversity of South Carolina (MUSC) and the Redox Biology Center of the University of Nebraska in Lincoln (UNL),Nebraska, which are two NIH COBRE (Center of Biological Research Excellence) initatives focused on research inredox biology. The course is planned to be annually held and will have the following major components: Studentsfrom MUSC, UNL and Karolinska Institutet Lecturers from MUSC, Karolinska Institutet and UNL Plannedlectures will contain subjects such as the following examples: "Glutathione Stransferases in redox regulation andglutathione dependent catalysis" "Nitric oxide (NO) signaling in relation to redox state" "Calcium signaling inoxidative stress and in relation to apoptosis" "Glutaredoxin and thioredoxin systems" "The concepts and effectsof redox cycling and selenoprotein reactivity" "Selenoproteomes and dedicated Cys and/or Secdependent redoxsystems" "Using protein crystallography to probe the function of redox active enzymes" "Redox activities ofproline in a cellular context" "The effects of metals on metabolism and oxidative stress in human disease" "Withthe sight on redox: glutaredoxin and thioredoxin systems in the ocular lens and their relation to cataract" "Redoxcontrol of ion channels" "How oxygen can be sensed in the carotid body" "Mitochondrial production of reactiveoxygen species in relation to human disease"

Teaching and learning activities : The course it is built upon a pedagogic framework of discussions betweengraduate students in redox biology with leading experts in the field, combined with cuttingedge lectures, trainingin oral presentation, career counceling sessions and a written exam for control of detailed basic knowledge in redoxbiology. It is the firm belief of the course organizers that this pedagogic framework should well support thestudents to obtain the learning objectives of the course. It should furthermore help the students to prepare for theirnext level of a career beyond the doctoral examination. The type of teaching will be: Morning sessions withlectures in basic concepts as well as cuttingedge frontline research findings in the field Afternoon sessions withstudent presentations followed by discussions between lecturers and students Career discussions and futureperspectives in the field of redox biology

Examination : The student skills are examined as follows: Evaluation of the degree of participation in studentlecturer discussions and the level of initiated comments and questions during those discussions (grade pass/notpass) Evaluation of the presentation of the student's own project (grade pass/not pass) Results at writtenexamination (at least 60% right answers for the grade of pass) Attendence during compulsory parts of the courseas well as the grade of "Pass" in all three parts of the examination must be fulfilled for a final grade of "Pass".

Compulsory elements : Absence from any part of the course (lectures, student presentations, career discussions,exam and award ceremony) is generally not accepted but could in special cases be compensated by an individuallytailored additional discussion and a special written examination organized by the course committee.



More information : Note: At this occasion the course will be held at the Medical University of South Carolina(MUSC) in Charleston, SC, USA, thus necessitating travel to the course during the weekend of May 1920 andreturn to Sweden during the weekend of May 2627. Travel support will be given to the home department atKarolinska Institutet (KI) with a flat rate of SEK 8.000 per doctoral student that comes from from KI. The givennumber of participants in this international course entails all participants from all sites. From Sweden a maximumnumber of eight (8) participants can be accepted to the course.

Course responsible : Elias Arnér

Department of Medical Biochemistry and Biophysics 0852486983

[email protected]

Contact person : Elias Arnér

Institutionen för medicinsk biokemi och biofysik 0852486983

[email protected]

Title : Causal Inference for Epidemiological Research




Specific entry requirements : The students are expected to have taken Epidemiology I, Epidemiology II,Biostatistics I, and Biostatistics II. Exceptions can be made if the students have taken other courses with anequivalent content.

Purpose of the course : This course aims to present causal theory and introduces how concepts and methods canbe understood within a general methodological framework.

Learning outcomes : After the course the student will be able to use counterfactuals to express and interpretcausal queries be able to judge when standard statistical methodology is appropriate for causal inference, andwhen it is not be able to use Directed Acyclic Graphs to describe and analyze complex epidemiological scenarios be able to use Marginal Structural Models to analyze longitudinal data, with additional help from a skilledstatistician

Contents of the course : Causal inference from observational data is a key task of biostatistics and of alliedsciences such as sociology, education, behavioral sciences, demography, economics, health services research, etc.These disciplines share a methodological framework for causal inference that has been developed over the lastdecades. This course presents this unifying causal theory and shows how biostatistical concepts and methods canbe understood within this general framework. The course emphasizes conceptualization but also introducesstatistical models and methods for timevarying exposures. Specifically, this course strives to a) formally definecausal concepts such as causal effect and confounding, b) identify the conditions required to estimate causaleffects, and c) use analytical methods that, under those conditions, provide estimates that can be endowed with acausal interpretation. The (causal) methods can be used under less restrictive conditions than the traditionalstatistical methods. For example, causal methods allow one to estimate the causal effect of a timevaryingexposure in the presence of timedependent confounders that lie on the causal pathway between exposure andoutcome.

Teaching and learning activities : Lectures and group discussions. Examination : There will be a takehome exam handed out at the last day of the course. Students who fail will be

given the opportunity to write at a maximum 2 reexams. Dates for the reexams will be announced later. Compulsory elements :

Number of students : 8 25 Selection of students : Eligible doctoral students will be prioritized according to 1) the relevance of the course

syllabus for the applicant's doctoral project (according to written motivation), 2) date for registration as a doctoralstudent (priority given to earlier registration date). To be considered, submit a completed application form. Give allinformation requested, including a short description of current research and motivation for attending, as well as anaccount of previous courses taken.

More information : Course dates are February 26, 28, March 2, 5 and 6. The course is extended over 2 weeks(but still 5 full course days) in order to promote reflection and reinforce learning.

Course responsible : Yudi Pawitan


[email protected]



Title : Clinical Research in Lipid Metabolism



Level : Doctoral level Responsible KI department : Department of Medicine, Huddinge

Specific entry requirements : Purpose of the course : The course constitutes an opportunity for the student to gradually increase his/her

understanding of clinical research in lipid metabolism during the course of a week. The purpose of the course is toprovide comprehensive as well as in depth knowledge in order for the student to be able to apply establishedmodels and methods used in this field in his/her own research.

Learning outcomes : After the course the students will be able to describe: 1. lipid and lipoprotein metabolism 2.diseases associated with lipid metabolism and their characteristics 3. approaches available and under developmentfor preventing or treating lipid disorders 4. models and laboratory methods used in lipid metabolism in in vivostudies

Contents of the course : Overview and new developments within the field of clinical research in lipid metabolism.Emphasis will be laid on cholesterol metabolism, lipoproteins, lipoprotein receptors and on the regulation ofenzymes involved in metabolism of cholesterol, bile acids, fatty acids and triglycerides. Genetic diseases and effectsof diet on clinical conditions such as atherosclerosis, obesity, diabetes, and gallstone disease will also behighlighted.

Teaching and learning activities : The course is comprised by lectures. Examination : The intended learning outcomes of the course will be assessed by a written examination on the last

day of the course. Compulsory elements : The lectures are mandatory. All information presented at the lectures is compulsory and

will be a significant basis for the written examination. A missed lecture has to be compensated for by completing anessay in accordance with instructions of the organizers.


doctoral project (according to written motivation) and 2) date for registration as a doctoral student (priority givento earlier registration date).

More information : The course is held in English and lectures and self studies will correspond to 40 working hours(1.5 credits). The location is the Karolinska Institutet at Karolinska University Hospital Huddinge in Flemingsberg. Amore detailed location will be announced in proximity to the course.

Course responsible : Sara Straniero

Department of Medicine, Huddinge

[email protected]

Contact person : Sara Straniero

Institutionen för medicin, Huddinge

[email protected]

Ylva Bonde Institutionen för medicin, Huddinge

[email protected]

Title : Career skills for scientists




Specific entry requirements : Purpose of the course : This course prepares PhD students for life after dissertation. You start to explore your

transferable skills and how to communicate them. You learn a lot about yourself and the many career paths thereare for PhDs. The course also gives you the opportunity to expand your contacts and network. This course givesyou the possibility to explore your interests, talents and skills. Course participants also get the opportunity to applyfor a one month financed internship at a company or organisation whithin life sciences.

Learning outcomes : After the course the participants should be able to discuss options in academic andnonacademic settings. The participants should be able to identify transferable skills achieved during doctoraltraining and be able to explain the value of these skills within as well as outside academia. They will also be able todescribe the financing procedure of research projects and discuss project management. They should also be able toapply what they have learned in the course to market their skills in different situations.

Contents of the course : The course includes an introductory reflection of the career options available for PhDsand researchers. This will be followed by sessions where academic and nonacademic career paths andentrepreneurial options are presented and discussed. The course covers financing of research activities, projectmanagement and networking exercises. In addition, the course includes the process and steps in a job applicationprocedure and how to use communication skills in various contexts.

Teaching and learning activities : The course will be highly interactive and will consist of lectures, discussions,individual projects and student presentations.

Examination : The participants will be examined thorugh oral group presentations and an individual writtenproject.

Compulsory elements : It is compulsory to attend all the lectures and workshops (except where clearly statedotherwise). Absence from compulsory parts will be compensated for according to instructions of the course directorwith an additional individual project.

Number of students : 25 35 Selection of students : Selection will be based on 1) PhD students who are in their third or fourth year of the

doctoral education 2) written motivation letter More information : The course starts on February 7 and ends at March 15. Course days are Wednesdays from

13.0017.00 during the first four occasions. The last two occasions (March 14 and 15) consists of examinations inhalf groups from 13.0017.00. The course takes place at campus Solna.

Course responsible : Hanna Jansson

Department of Learning, Informatics, Management and Ethics 0852483861

[email protected]

Contact person : Anethe Mansen

Universitetsförvaltningen 08524 863 76

[email protected]

Kerstin Beckenius Universitetsförvaltningen


Title : Interview techniques in health and care research



Level : Doctoral level Responsible KI department : Department of Clinical Neuroscience

Specific entry requirements : Purpose of the course : The course aims to provide course participants with a broad understanding for a research

interview; i.e. planning and conducting a research interview within a research program. In addition the participantswill be enabled to gain an increased understanding and a professional attitude of the researcher as an instrumentfor data collection which can be applied and potentially enhance the quality of data in future research interviews.

Learning outcomes : After the course the student is expected to be able to (a) Identify and understand thecontent of a research interview. (b) Demonstrate and master necessary interview tools in order to, (c)Independently, analyze and adapt this knowledge and practical skills in order to compose a research interview; i.e.planning, designing, carrying out and critically evaluating the interview. (d) Communicate and give feedback toother students' research interviews Contents of the course : a. different perspectives and knowledge for conducting interviews b. the role ofempathy in interview communication c. the researcher´s role as an instrument in data collection d.intersubjectivity, biases and ethical considerations of research interviewing e. how to plan an interview guide f.how to formulate questions g. how to conduct an interview with respect for culture and vulnerable groups

Teaching and learning activities : The course will be offered parttime, usually full Days from 9 a.m. to 4 p.m.,12 days weekly including lectures, video demonstrations covering various interviews and interview techniques,interview technique training seminars in small groups, supervision seminars (interview guides) with literaturediscussions and selfmonitored studies and practice. Since interview training is a process which requires testingin vivo, improvements, reflection between training the course covers approximately a 5week period. Examination : Examination will consist of an interview guide and of an individually taped documentation of aninterview with a research subject in the own research field presented in the course group. In addition the courseparticipant will critically analyze a fello student's videotaped interview. The presentation will furthermore be withina theoretical frame of reference including the course literature, discussing interviews, interview techniques,potential biases challenging the quality of the interview responses. The reason behind choosing this kind ofexamination is that it has been proven to give earlier interview studentgroups valuable learning experiences whichimmediately can be applied in the respective research area.

Compulsory elements : The education will be compulsory scheduled all through the course. If the student isunable to be present he/she has to consult the course leader/examiner for adequate opportunities to recovermissed hours (usually in the form of written assignments, except for practical training and examination with thevideotaped interviews).



More information : The course will take place at Huddinge Campus. The course is given full days; i.e. 9 am 4pm the following dates: (1) Wednesday April 4th; (2) Thursday April 5 th; (3) Wednesday April 11th; (4)Wednesday April 18th; (5) Wednesday May 2nd; (6) Thursday May 3rd.

Course responsible : Gunnel Backenroth

Department of Clinical Neuroscience

[email protected]

Contact person :

Title : Writing science and information literacy



Level : Doctoral level Responsible KI department : Karolinska Institutet University Library

Specific entry requirements : Purpose of the course : The aim of the course is to develop the medical scientific writing skills and information

literacy of the participant. Learning outcomes : After the course, you will be able to demonstrate: understanding of how to write an original

scientific article and submit it for publication. the ability to write other types of texts required for a scientificcareer. the ability to give, take and make use of constructive criticism. the ability to search and manage themedical sciences literature in a structured way. the ability to use resources which facilitate choosing a journal topublish your research. and be able to describe aspects of postpublication evaluation and processing of the medicalsciences literature.

Contents of the course : Basics of scientific writing, Searching the literature, Writing an original scientific paper,Supporting the text, Managing the literature, Scientific writing in other contexts, Choosing a journal, Thepublication process, Evaluating published science.

Teaching and learning activities : This 100% ONLINE course (there is also a KI Campus version with coursecode 1391) will be held using the learning management system Ping Pong. Content will be learnt with variouslearning objects and learning practiced by exercises. Formative feedback will be given by teachers/peer/selfassessment. Scientific writing, literature management and other ITrelated skills will be developed in the context ofscientific communication.

Examination : The intended learning outcomes are assessed in the summative examination. Participants will writeand rewrite a grant application and popular science summary based on teacher and peer feedback. Participants willalso complete a number of assignments which demonstrate their ability to use relevant IT resources in a context ofscientific writing and communication.

Compulsory elements : There will be a number of obligatory assignments and assessments to be completed. Number of students : 20 22


More information :

Course responsible : David Herron

Karolinska Institutet University Library 08524 841 13

[email protected]

Berzelius 7B

17177 Stockholm

Contact person :

Katarina Amcoff Karolinska Institutet universitetsbibliotek


Title : Basic Course in Medical Statistics a distance course








Teaching and learning activities : The course is a hybrid course mixing online studies with facetoface inclassfinal seminars. The course activities are video lectures, selfstudy, selfassessment exercises, individual computerbased exercises, and statistical software demonstration videos in Statistica and SPSS. The first and last day of thecourse will be facetoface with an introduction the first day and seminars and group discussions the last day.

Examination : Correct answers on the individual computer based exercises. The doctoral students will have todemonstrate their ability to recognize, critically examine and discuss the statistics presented in the medical articlesduring the seminars.

Compulsory elements : Attendance is mandatory for the seminars on the last day of the course. If the student isabsent, he or she will have priority for admission to the seminars the next time the course is offered. If a studentjoins the course when physically located in another country it is the student's responsibility to contact the coursedirector in advance to agree on an individual supplementary task to compensate for the absence.


Please make sure that you have entered the correct registration date for doctoral education in your personal profile. More information : Course dates at KI: February 12th (not mandatory) and February 23rd (mandatory).



[email protected]

Contact person : Elisabeth Löfgren


[email protected]

Title : Basic Course in Medical Statistics a distance course








Teaching and learning activities : The course is a hybrid course mixing online studies with facetoface inclassfinal seminars. The course activities are video lectures, selfstudy, selfassessment exercises, individual computerbased exercises, and statistical software demonstration videos in Statistica and SPSS. The first and last day of thecourse will be facetoface with an introduction the first day and seminars and group discussions the last day.

Examination : Correct answers on the individual computer based exercises. The doctoral students will have todemonstrate their ability to recognize, critically examine and discuss the statistics presented in the medical articlesduring the seminars.

Compulsory elements : Attendance is mandatory for the seminars on the last day of the course. If the student isabsent, he or she will have priority for admission to the seminars the next time the course is offered. If a studentjoins the course when physically located in another country it is the student's responsibility to contact the coursedirector in advance to agree on an individual supplementary task to compensate for the absence.


Please make sure that you have entered the correct registration date for doctoral education in your personal profile. More information : Course dates at KI: May 7th (not mandatory) and May 18th (mandatory).



[email protected]





[email protected]

Title : Write your research results and get them published



Level : Doctoral level Responsible KI department : Department of Women's and children's health

Specific entry requirements : None. Purpose of the course : The purpose of the course is to impart knowledge and practical experience in scientific

writing, based on own research, including manuscript, abstract and cover letter writing and scientific poster design. Learning outcomes : AFTER ATTENDING THE COURSE, THE DOCTORAL STUDENT SHOULD BE ABLE TO:

Explain the characteristics and disposition of different written presentation media and decide which forum is themost suitable for a specific text Understand, and apply, the terminology associated with scientific writing Writean abstract Use the correct structure and language to compose a scientific paper, following the editorialrequirements Revise a manuscript according to a checklist with the most common language and structuremistakes in scientific writing Use the focus points in a scientific paper (where the readers focus their reading) Identify the main scope and focus of the research and summarize information aligned to the target group Applythe structure of popular science writing and use popular science as a tool for presentations Give a posterpresentation Design a scientific poster and reflect upon structure, language and style Understand the ethics inpublication Use the software EndNote for reference management Search for references in databases (e.g.PubMed) and decide what sources are reliable Respond to the reviewer's comments Write a cover letter Reflect on own development as a writer of different texts during the course

Contents of the course : THE MAIN SCOPE OF THE COURSE is how to write about research in different contextsand forums. THE CONTENT OF THE COURSE: 1. Terminology associated to scientific writing 2. Designing andwriting a) a poster b) an abstract c) a draft for a research paper d) a cover letter e) a reply to the reviewer´scomments f) a cover letter g) a popular science paper 3. The writing process: structure, language, style 4. Editorialrequirements of different journals 5. Summarizing and presenting information aiming at the target audience 6.Identifying the main scope of a research project 7. References and reference management (EndNote software) 8.Data base search 9. Basic rhetoric for poster presentations 10. References 11. Ethics in publication

Teaching and learning activities : Lectures, seminares, writing exercises, group assignments and practicalexercises. As part of the learning process, the Ph.D students will be members of inclass review groups, givingfeedback to their colleagues.

Examination : 1) Written assignments reflecting the intended learning outcomes of the course: draft for scientificpaper, popular science paper, poster, cover letter, and abstract. All assignments can be based on own research (ifapplicable). 2) Evaluation sessions, where the PhD students give each other feed back on the written assignmentsas a part of the learning process 3) Poster presentation, where the PhD students present their posters to a smallgroup of course participants (there are no presentations in front of a larger group)

Compulsory elements : Lectures, workshops, evaluation sessions, and group assignments as well as all writtenassignments. Absence can be compensated: a) during next course occasion b) individual assignments


doctoral project (according to written motivation), 2) date for registration as a doctoral student (priority given toLATER registration date).

More information : Welcome to apply for the writing course Write your research results and get them published!The course includes manuscript writing, poster design and presentation, cover letter writing, abstract writing andpopular science writing. The focus is on scientific writing (manuscript, abstract and poster). The popular sciencewriting is covering the skills you need in order to successfully write a popular science summary for a project plan orto apply for grants. The course will be given in central Stockholm, in Gamla Brogatan (close to Hötorget). Pleaseaddress all questions to: [email protected] or phone: 0707890607

Course responsible : Anna Hildenbrand Wachtmeister

Department of Women's and children's health 0707890607

[email protected]

Contact person : Anna Hildenbrand Wachtmeister

Institutionen för kvinnors och barns hälsa 0707890607

[email protected]

Lalit Kumar Institutionen för kvinnors och barns hälsa

[email protected]

















[email protected]



[email protected]


[email protected]

















[email protected]



[email protected]


[email protected]

















[email protected]



[email protected]


[email protected]

Title : Klinisk forskning och Good Clinical Practice: protokoll,informerat samtycke och ansökan i enlighet med lagar/regler



Level : Forskarnivå Responsible KI department : Department of Clinical Sciences, Danderyd Hospital

Specific entry requirements : Purpose of the course : Kursen ger god kunskap om det regelverk som gäller vid klinisk forskning

(registerforskning och kliniska prövningar). Detta är nödvändig kunskap för alla som bedriver klinisk forskning. Learning outcomes : Kunskaper om Good Clinical Practice (GCP) samt forskningsetik (Helsingforsdeklarationen).

Kursen täcker de krav på GCPutbildning som Läkemedelsverket ställer för att delta i en kliniskläkemedelsprövning. Deltagaren ska efter genomgången kurs kunna delta som en prövare i en klinisk prövning. Kunskaper om hur man praktiskt ansöker om klinisk prövning till Regional etikprövningsnämnd, Läkemedelsverketsamt till Datainspektionen. Deltagaren ska efter genomgången kurs kunna skriva en ansökan till Regionaletikprövningsnämnd och veta hur man skriver sådan till Läkemedelsverket samt till Datainspektionen. Kunskaperrörande regelverket för klinisk prövning (Etikprövningslagen, Personuppgiftslagen, Biobankslagen,Läkemedelsverkets författningssamling m fl). Deltagaren ska efter genomgången kurs känna till regelverket för atträtt kunna planera en klinisk prövning. Beräkning av deltagarantalet i en studie. Deltagaren ska eftergenomgången kurs veta vad som påverkar studiestorlek och kunna ta fram rätt underlag för att kunna beräknadetta. Kunskap om kraven att registrera en studie i publik databas (Clinical Trial Registry) samt hur man gör föratt få en studie publicerad. Deltagaren ska efter genomgången kurs kunna registrera en studie i en publik databas. Kunskaper om de krav som ställs vid registerforskning. Deltagaren ska efter genomgången kurs känna tillregelverket vid registerforskning.

Contents of the course : Föreläsningar om det regelverk som gäller vid klinisk forskning (registerforskning ochkliniska prövningar): Helsingforsdeklarationen, GCP, Etikprövningslagen, Personuppgiftslagen, Biobankslagen,Läkemedelsverkets författningssamling, Codex: regler och riktlinjer för forskning (codex.vr.se) m fl. Beräkning avpatientantal. Genomgång av ansökningshandlingar till Regional etikprövningsnämnd, Läkemedelsverket ochDatainspektionen. Hur man skriver en etikansökan och författar en patientinformation. Hur man gör för attregistrera en prövning i ett Clinical Trial Registry samt regler för publicering. Praktiska GCPråd på hur mangenomför en klinisk prövning. Kursen lämpar sig också väl för de som bedriver klinisk registerforskning.

Teaching and learning activities : Föreläsningar, diskussioner och seminarier samt examinationsuppgift(studiesynopsis, etikansökan och patientinformation).

Examination : Doktorandens examinationsuppgift kommer att bedömas och diskuteras i seminarieform. Compulsory elements : Närvaro vid undervisning/seminarier samt inlämning av examinationsuppgift

(studiesynopsis, etikansökan och patientinformation). Vid frånvaro från schemalagda aktiviteter måste deltagarengenom kompletterade extra inlämningsuppgift kunna styrka motsvarande inhämtning av kunskap.


motivering), 2) datum för doktorandregistrering (där tidigare registreringsdatum har förtur) More information : Kursen består av föreläsningar och arbete i seminarieform på Danderyds sjukhus 20180205

07 + 20180209. Examinationsuppgiften (studiesynopsis, etikansökan och patientinformation) genomförs 2018020608 och lämnas därefter in för individuell bedömning och återkoppling. Examinationsuppgiften kommer ocksåatt diskuteras och bedömas i seminarieform.

Course responsible : Thomas Kahan

Department of Clinical Sciences, Danderyd Hospital 08 123 568 61

[email protected]

Contact person : Nina Ringart

Institutionen för kliniska vetenskaper, Danderyds sjukhus 08123 564 12

[email protected]

Title : Sickness absence research: theories, methods, and concepts




Specific entry requirements : Purpose of the course : The course aims to provide participants with basic and wide competence about current

research on sickness absence, regarding different types of study designs, data, and analytical approaches withindifferent scientific disciplines, as a bases for own reserach on sickness absence/disability pension.

Learning outcomes : After succesfully completing this course the doctorial student will be able to: showknowledge about the area of sickness absence, in terms of what research that is conducted in various scientificdisciplines (e.g. economics, sociology, medicine, management, psychology, law, philosophy, public health) and tobe able to relate own research project to this, according to a classification presented at the course. show basicknowledge about different scientific methods used in research on sickness absence, with respect to study design,data collection, and data analysis. show knowledge about risk factors for sickness absence, consequences of beingsickness absent, and factors that hinder or promote return to work. show basic knowledge on international as wellas historical aspects of sickness insurance systems. search for relevant studies in litterature databases. participate in scientific discussions, verbally and in writing, regarding sickness absence and issues in the researcharea, with regard to perspectives, theories, explanatory models, and concepts.

Contents of the course : This multidisciplinary course covers knowledge of sickness absence/disability pensionwith a focus on theories, methods, and concepts used in such research. Among other things, the theories andmethods used in research in medicine, sociology, economics, psychology, law, and management will be presented.Furthermore, the different perspectives within the research area will be considered such as a gender perspectiveand a social class perspective.

Teaching and learning activities : The course begins with three full, mandatory days of lectures by national andinternational well known researchers in the field and of group work. Thereafter, nine weeks with individual work(studying literature, write a paper (with focus on own project), logbook, etceteras) and group meetings withdiscussions of central scientific articles within the research area, will follow. Group discussion takes place either atfacetoface meetings, Skype, or discussion forums via KIs' webbased forum. After that, the whole course meetsagain, for three additional mandatory days of lectures, group work, and seminaries about the papers the studentshave written.

Examination : Examination will take place at the seminars on all the papers during the three last days of thecourse. Each participant is to actively demonstrate that he/she has acquired the above knowledge, skills andattitudes in all the roles as respondent, opponent, and seminar participant. Students who do not obtain a passinggrade in the first examination will be offered a second examination within two months of the final day of the course.

Compulsory elements : To pass the course, active participation in all course days in Stockholm is required, takingactive part in the group work and discussions in between the course days, write a summary of the individuallogbook, and submitted a paper in due time. Any absence is to be compensated by arrangement with the courseleader and may vary depending on which course sections that have been missed.

Number of students : 10 15 Selection of students : Acceptence to the course is based in the relevance of the course for the PhD project

(based omn given motivation) More information : The course starts with three intensive, fully scheduled days + evenings in Stockholm, followed

by several weeks of individual and group work. Thereafter, additional three days in Stockholm, including seminars.Several lectures will be given, covering different aspects and disciplines within the research areas.

Course responsible : Kristina Alexanderson

Department of Clinical Neuroscience 08 524 832 00

[email protected]

Division of Insurance Medicine Karolinska Institutet

171 77 Stockholm

Contact person :

Emilie Friberg Institutionen för klinisk neurovetenskap


Title : Human physiology an overview



Level : Doctoral level Responsible KI department : Department of Physiology and Pharmacology

Specific entry requirements : Purpose of the course : KI is a medical university with research and education in medicine and health. All PhD

students have to obtain basic knowledge regarding the human body in health and disease in case they lack basichigher education knowledge in the field of medicine. The aim of the course is to give PhD students without amedical background a basic overview and introduction to human physiology. The students will gain a basicunderstanding of how the human organ systems function and interact under normal conditions. The contentcovered in this course will be useful for further studies where knowledge about human biology is of value.

Learning outcomes : After completing the course, the student will gain a basic understanding of how the humanorgan systems function and interact under normal conditions. The content covered in this course will be useful forfurther studies where knowledge about human biology is of value. More specifically, the student will be able to: Demonstrate knowledge and understanding of basic functions and interactions between organ systems in thehuman body. Demonstrate a critical and scientific approach to literature sources for the different course tasks.

Contents of the course : Overview of cellular and integrative physiology Basic anatomy Biochemistry andcell biology Nervous system Endocrinology Digestive system Cardiovascular physiology Renal physiology Respiration Basic immunology

Teaching and learning activities : Different learning methods such as problem based learning, lectures and ahandson human lab session will be used. Full time during two consecutive weeks.

Examination : To pass the course, the student must demonstrate that the learning outcomes have been achieved.Oral and written examinations are used for student assessment.

Compulsory elements : Examinations and the handson human lab are required. Students that are absent duringthe quiz or the lab must perform a makeup quiz/lab. Students that are absent from the exam or do not obtain apassing grade in the first examination will be offered a second examination.

Number of students : 20 25 Selection of students : Selection is based on 1. the date of the registration and 2. the written motivation

More information : Conducted at KI Campus Solna

Course responsible : Jessica Norrbom

Department of Physiology and Pharmacology

[email protected]

Contact person :

Title : Methods for statistical analysis: From analysis of variance tomultilevel modeling




Specific entry requirements : Documented knowledge about basic statistics Purpose of the course : To give graduate students an opportunity to learn to use a number of statistical methods.

Learning outcomes : After the course the participants should be able to conduct the following statistical analyses:(1) Analysis of variance; (2) Multiple regression analysis; (3) Risk and Oddsratios; (4) Logistic regression; (5)Cox regression; (6) Factor analysis; (7) Structural Equation Modeling; (8) Multilevel Modeling

Contents of the course : The above mentioned methods for statistical analysis. Teaching and learning activities : The course contains lectures and computer exercises. The lectures will cover

the theoretical material and contain relevant examples. In the computer exercises the methods of analysis will beused on given data. SPSS (or, on request, R) will be used in the computer exercises. No support for SAS will beavailable.

Examination : The participants will conduct the analyses that are included in the course and present and interpretthe results from these analyses in an individual examination report.

Compulsory elements : No compulsory elements. Number of students : 18 23

Selection of students : Selection will be based on 1) the relevance of the course syllabus for the applicant'sdoctoral project (according to written motivation), 2) date for registration as a doctoral student (priority given toearlier registration date).

More information : Live lectures/workshops on the following dates: 19/4, 26/4, 3/5, 9/5, 17/5, 24/5, 31/5.Submission of examination task: 1/6. Besides these occasions, the participants are asked to watch recordedlectures on the internet, one lecture (35 hours) before each workshop.

Course responsible : Kimmo Sorjonen


[email protected]

Contact person :

Title : Basic Laboratory Safety




Specific entry requirements : Experience of and/or education in laboratory work Purpose of the course : The purpose of the course is to give the students an understanding of risks and of

principles in safety measures in the biological laboratory, as well as a consciousness about general and individualresponsibilities for the planning and execution of applicable safety measures. The purpose is also to develop skills inperforming risk analyses and writing up risk assessments.

Learning outcomes : After successfully completing this course you as a student should be able to evaluate therisks associated with experiments in the laboratory. The hazards could originate from chemicals, microbiologicalagents, cell cultures and human blood/tissues. You should also be able to identify the needs for suitable personalprotective equipment, routines for waste management and transport. In addition, you should be familiar with theregulatory framework that governs these topics, the basic needs of a safe laboratory, and be able to identify thechain of responsibilities.

Contents of the course : The course aims at giving theoretical and practical knowledge on chemical and biologicalaspects of laboratory safety. Topics will deal with writing risk assessments, chemical health risks including allergy,cancer and flammable agents, handling and storage of dangerous chemicals, handling of microorganisms and cellcultures including human blood and tissue samples, laboratory acquired infections, biosafety measures includingpersonal protection devices, ventilated workplaces, genetically modified microorganisms, biosecurity and dual use,transport of dangerous goods and waste management.

Teaching and learning activities : The information will be given as lectures, group discussions, practicalsessions, webtutorials and computer sessions during a total of six days.

Examination : The examination is based on an individual written examination, the active participation in a grouppresentation and the risk assessment. One needs a pass of each of these three assessments in order to pass thecourse.

Compulsory elements : Presence during some of the course activities, marked in the schedule, is compulsory.Students cannot compensate for absence during compulsory activities, but are referred to coming courses for theseactivities.

Number of students : 30 40 Selection of students : Selection will be based on 1) date for registration as a doctoral student (priority given to

earlier registration date), 2) the relevance of the course syllabus for the applicants doctoral project (according towritten motivation).

More information :

Course responsible : Maria Johansson

Department of Microbiology, Tumor and Cell Biologi

[email protected]

Contact person : Annika Carlsson

Institutionen för mikrobiologi, tumör och cellbiologi

[email protected]

Title : Basic Laboratory Safety




Specific entry requirements : Experience of and/or education in laboratory work Purpose of the course : The purpose of the course is to give the students an understanding of risks and of

principles in safety measures in the biological laboratory, as well as a consciousness about general and individualresponsibilities for the planning and execution of applicable safety measures. The purpose is also to develop skills inperforming risk analyses and writing up risk assessments.

Learning outcomes : After successfully completing this course you as a student should be able to evaluate therisks associated with experiments in the laboratory. The hazards could originate from chemicals, microbiologicalagents, cell cultures and human blood/tissues. You should also be able to identify the needs for suitable personalprotective equipment, routines for waste management and transport. In addition, you should be familiar with theregulatory framework that governs these topics, the basic needs of a safe laboratory, and be able to identify thechain of responsibilities.

Contents of the course : The course aims at giving theoretical and practical knowledge on chemical and biologicalaspects of laboratory safety. Topics will deal with writing risk assessments, chemical health risks including allergy,cancer and flammable agents, handling and storage of dangerous chemicals, handling of microorganisms and cellcultures including human blood and tissue samples, laboratory acquired infections, biosafety measures includingpersonal protection devices, ventilated workplaces, genetically modified microorganisms, biosecurity and dual use,transport of dangerous goods and waste management.

Teaching and learning activities : The information will be given as lectures, group discussions, practicalsessions, webtutorials and computer sessions during a total of six days.

Examination : The examination is based on an individual written examination, the active participation in a grouppresentation and the risk assessment. One needs a pass of each of these three assessments in order to pass thecourse.

Compulsory elements : Presence during some of the course activities, marked in the schedule, is compulsory.Students cannot compensate for absence during compulsory activities, but are referred to coming courses for theseactivities.


earlier registration date), 2) the relevance of the course syllabus for the applicants doctoral project (according towritten motivation).

More information :

Course responsible : Maria Johansson


[email protected]

Contact person : Annika Carlsson


[email protected]

Title : Biobanking as a resource for biomedical research




Specific entry requirements : Nej Purpose of the course : This course aims to provide practical knowledge to start biobanking with state of the art

quality comprising ethics, legal aspects, sampling handling and logistics. Furthermore the course aims to enable thecourse participants to get insight in and knowledge about how to collect human tissue samples and associated data,about how to apply technology advancements such as next generation sequencing, proteomics and metabolomicsto harness biological information from biobanked material such as tissues and liquid biopsies and finally to getinsight into successful research projects where biobanking in combination with large scale analysis is having directimpact on health care. .

Learning outcomes : At the end of the course the student should: Understand the value of biobanks and be ableto explain how to use these rich sources of samples and related data. Understand the legal and ethical frameworkrelated to biobanks and how to utilize biobanked samples in future national and international projects, Haveinsight and knowledge about how to start a new study and understand the impact of quality and standardization ondownstream applications, Understand and explain the need for a secure IT structure in order to ensure the sampledonors integrity with a full traceability of samples and data, Discuss own or other's research projects related tobiobanked samples.

Contents of the course : 1. Practical knowledge to enable biobanking including Ethical and Legal aspects ITinfrastructure Required documentation and stakeholders Biobank service; available infrastructures 2. How tobiobank with high quality from various sources such as: Blood/plasma/serum/urine PBMC Single cells Tissues 3. Examples of how to apply molecular technologies to harness information Proteomics of plasma and tissues Metabolomics of plasma, serum and urine Sequencing of circulating tumor DNA/RNA Single cell sequencing ofcirculating tumor cells and tissues DNA and RNA sequencing of tumor tissues Epigenetics of blood and tissues 4.The value of applying quality registries to biobanked material

Teaching and learning activities : Lectures Exercises Field trip (visiting a biobank) Final seminar withpresentations and discussions about the course assignment (either a predefined biobank study or an example fromown research)

Examination : Presentation and discussion of the course assignments, either a predefined biobank study or anexample from own research. All learning outcomes will be covered.

Compulsory elements : Taking part in all scheduled activities: lectures, field trip and presentation/examination.Compensation according to the instructions of the course director.


doctoral project (according to written motivation), 2) date for registration as a doctoral student (priority given toearlier registration date).

More information : Monday Friday 9:0016:00 Venue: Wargentin, Dept of medical epidemiology andbiostatistics, Campus Solna.

Course responsible : Gunnel Tybring


[email protected]

Contact person : Johan Lindberg

Institutionen för medicinsk epidemiologi och biostatistik

[email protected]

Title : Breast Cancer: Research and treatment



Level : Doctoral level Responsible KI department : Department of OncologyPathology

Specific entry requirements : Basic knowledge within the field of cancer biology is required Purpose of the course : The course aims to provide an overview of the molecular characterization, epidemiology

and current treatment of breast cancer. The overall purpose is to form a bridge between preclinical and clinicalaspects of breast cancer biology and oncology and to enable the PhD students to obtain a deeper understanding ofall aspects of the breast cancer problem.

Learning outcomes : At the end of the course the students need to be able to show a thorough understandingof the basic foundations of breast cancer biology the ability to discuss and understand advanced conceptsand problems in breast cancer biology to understand and be able to discuss important problems to solve in breastcancer in order to improve diagnosis, prevention of disease, treatment and quality of life.

Contents of the course : This course is a basic introduction to modern breast cancer research and treatment andit is recommended to all PhD students within basic, epidemiologic and clinical breast cancer research. The coursewill describe our current understanding of breast cancer from molecule to patient, eventually also discussing itsmanagement, pathology, prevention and treatment. The topics of the course include genetics, the cell cycle,apoptosis, immunology, diagnostics and treatment, and pathology. All topics will be presented from the breastcancer perspective. There will be focus on breast cancer biology and oncology, including molecular genetics,curative treatment and palliative care, psychosocial aspects of cancer, ethics and epidemiology.

Teaching and learning activities : The course consists of lectures, group seminars, group discussions anddemonstrations.

Examination : To pass the course the students must show that they have reached the learning outcomes of thecourse. This will be assessed by a written individual examination with a focus on understanding of concepts,relations and how problems are dealt within breast cancer research and treatment.

Compulsory elements : All seminars and demonstrations are compulsory, also some lectures, as well as thewritten examination. Single missed occasions can be compensated during the course after discussion with thecourse director.



More information : Information about the venue of the course will be provided to the students in due time.

Course responsible : Antroula Papakonstantinou

Department of OncologyPathology

[email protected]

Contact person :

Title : Calcium signaling



Level : Doctoral level Responsible KI department : Department of Clinical Science and Education, Södersjukhuset

Specific entry requirements : Purpose of the course : The aim of this course is to enable the students to get an insight in the fundamental

mechanisms of the regulation of cellular Ca2+ homeostasis, the generation and the decoding of Ca2+ signaling, theprinciples of the methods for measuring Ca2+ concentrations in different cellular compartments, and the generalroles of Ca2+ signals in mediating cellular functions.

Learning outcomes : After the course the students should be able to: 1. Critically analyze and interpret how thedifferent constituents of the Ca2+ signaling toolkit participate in the generation and decoding of Ca2+ signals, andin maintaining Ca2+ homeostasis. 2. Choose appropriate methods for studying different aspects of Ca2+ signaling 3. Critically analyze the existing literature on Ca2+ signaling, generate new ideas and put forward new hypotheses. 4. Design new studies on Ca2+ signaling in the context that is relevant to the research areas of the studentsthemselves

Contents of the course : 1. Phospholipase C and inositol 1,4,5 trisphosphatemediated signaling. 2. Identity androles of the molecular players involved in Ca2+ and phospholipidmediated signaling. 3. Preparation of Ca2+buffers. 4. Principles of methods used in the study of calcium and phospholipid signaling including fluorescenttechniques, electrphysiology and imaging techniques. 5. Regulation of ion channels involved in Ca2+ signalingincluding voltage sensitive channels, Transient Receptor Potential channels, store operated channels andintracellular C a2+ channels. 6. Roles of Ca2+ and phospholipid mediated signaling in cellular processes including insecretion and apoptosis. 7. Mechanism of generation and decoding of Ca2+ signals. 8. Spatial and temporal aspectsof Ca2+ signaling. 9. How to pick research problems in the areas of Ca2+ and phospholipid signaling and how toapproach the problems.

Teaching and learning activities : This course will follow the principles of active learning including the sevensteps problembasedlearning (PBL), and flipped classrooms. Emphasis will be on selfdirected learning throughproblemsolving in small groups rather than on cathedral lectures. Generous smallgroup interactive "lecturesessions" by resource personnel with ample time for questions and answers will be provided. Participants will workon selected problems designed to be starting points, in groups of about ten participants, under supervision oftrained facilitators who will be available during all of the sessions. Participants will be provided with an outline ofthe objectives, areas expected to cover, and reprints of selected learning materials.

Examination : Each student must submit a research proposal in the area of Ca2+ signalling where they willcritically analyze the existing literature, identify the gaps in the existing knowledge, put forward a new hypothesis,and choose appropriate methods to test the hypothesis. They will use conventional headings like: specific aims,background, methods, significance, and references. The proposal should be at least one A4 page long, but nolonger than three pages. Compulsory elements : Attendence in all the sessions is obligatory. In case of absence, the participant will haveto submit written reports specified by the coursesupervisor, to compensate for the absence.



More information : The course will be held at the Department of Clinical Science and Education, Södersjukhuset(Metro Skanstull, Bus number 3 to the entrance of the Södersjukhuset). The course will start every day at 09:00and end by latest 16:00. Lunch break 12:0013:00.

Course responsible : Shahidul Islam

Department of Clinical Science and Education, Södersjukhuset 086163950

[email protected]

Contact person : Joseph Bruton

Institutionen för fysiologi och farmakologi

[email protected]

Title : Intermediate Medical Statistics: Regression models




Specific entry requirements : Basic Medical Statistics (or equivalent) Purpose of the course : The aim of the course is to introduce intermediate statistical methods and to facilitate

acquirement of skills that involve handson data analysis using statistical software. Learning outcomes : After successfully completing this course students are expected to be able to: Understand

the basic theory behind the statistical methods introduced in the course and to evaluate their applicability andlimitations. Choose a suitable statistical model for assessing a specific research hypothesis using data from amedical science study, evaluate the fit of the model, and interpret the results. Apply the methods discussed in thecourse on real data.

Contents of the course : The course is an introduction to more advanced statistical methods and requires thatthe student is familiar with the statistical concepts of descriptive and inferential statistics, and has some basicknowledge of linear regression. The course covers intermediate regression analysis, oneway and twoway analysisof variance, repeated measures ANOVA, logistic regression, and introduction to survival analysis. Conceptsexamined in this course include dummy variables, confounding variables, interaction between variables, influentialobservations and model selection.

Teaching and learning activities : The course consists of lectures, group discussions and assignments solvedindividually and in groups. Some group discussions and exercises are compulsory.

Examination : Assessment of the intended learning outcomes by a passing grade on the computer basedexercises, and active participation in the final seminar and article presentations.

Compulsory elements : Computer based exercises, seminars, article presentations and some lectures aremandatory. The course leader assesses whether and if so, how absence can be compensated.



More information : The course will consist of three or four scheduled whole days per week for two weeks. Coursedates are: April 9, 10, 12, 13, 16, 17 and 20.



[email protected]





[email protected]

Title : Analysis of genome wide association data




Specific entry requirements : Knowledge corresponding to Biostatistics I: Introduction for epidemiologists andEpidemiology I: Introduction to epidemiology or equivalent courses.

Purpose of the course : The aim is to enable students to independently perform a complete genome wideassociation study (GWAS) analysis in a computationally effective and statistically correct manner.

Learning outcomes : After the course the student should be able to execute a standard genome wide associationstudy (GWAS) analysis using various tools (Linux, plink, R, among others). More specific the student should be ableto: Create directories, move files and perform other standard tasks using Linuxtype commands. Performstandard quality control procedures and filter data accordingly using plink, define the logic behind each qualityassessment and explain why high quality data is essential. Perform tests of association and apply multiple testingcorrection, interpret and discuss the result. Investigate the presence of biases, identify reasons for their presenceand manage different ways to correct for these. Use the language R to read and write files, and to illustrateresults from each step of the GWAS analysis. Perform secondary analysis and review the results.

Contents of the course : The course follows a standard GWAS analysis of a real data set of a complex trait, fromreceiving the data to processed and illustrated association results. During the course the student will use multipledifferent tools and computer languages.

Teaching and learning activities : The course focuses on active learning and includes introductory lectures,practical hands on analysis of GWAS data sets as well as group discussions.

Examination : To pass the course the student must fulfill the learning outcomes. This will be assessed through awritten individual report outlining the commands used and discussing their relevance as well as the achievedresults.

Compulsory elements : The individual examination (summative assessment). Number of students : 8 25


More information : Course dates are March 8, 9, 12, 13 and 14. The individual examination will be performed asa takehome examination.

Course responsible : Boel Brynedal


[email protected]


[email protected]

Nobels väg 13

17177

Stockholm

Title : Present your research!




Specific entry requirements : None Purpose of the course : The purpose of the course is to enable doctoral students to obtain knowledge and

practical experience in presenting own research orally; adapted to different presentation formats, target groups,supporting media and situations, as well as to reflect on the development of own presentation skills.

Learning outcomes : After attending the course, the doctoral student should: 1. Be able to design an oralpresentation in an asequate way. 2. Be able to design and use supportive media for a successful presentation. 3.Know the basics of presentation techniques and rethoric. 4. Have gained knowledge on how to interact with theaudience.

Contents of the course : The scope of the course is to design and give oral presentations of your research resultsin different contexts. The main content of the course: 1. DESIGN AND DISPOSITION OF AN ORAL PRESENTATION(e.g. poster presentation, short presentation of research results): a. Goals and aims b. Structure c. Simplificationsto enhance understanding d. Choice of pictures e. Language f. Time management 2. PRESENTATION TECHNIQUESAND RHETORIC FOR ORAL PRESENTATIONS: a. Body language and posture b. Language and pace c. How toprepare yourself for a presentation d. How to remember what you want to present e. Building confidence (be lessnervous) to present f. What to avoid doing during a presentation g. How to deal with questions from the audience 3. DESIGN AND USE OF SUPPORTING MEDIA FOR A PRESENTATION: a. Power Point slides including introduction topower point b. Scientific poster c. Flipchart and other supporting media 4. INTERACTION WITH THE AUDIENCE: a. Catching the audience's attention b. How to address the audience c. Keeping the audience's attention for alonger period of time d. Communicating with the audience e. How to make the audience trust you f. Preparing thepresentation with different audiences in mind g. Different learning styles which influences the audience's attention h. How to impress your audience i. Attention curve of the audience j. How to ease the learning of the audience 5.PRACTICAL EXERCISES: a. Presenting in front of an audience: i. Poster presentation ii. Presentation of student'schoice iii. Elevator Pitch iv. Power point presentation v. Video recording of presentation with feedback b.Presentation exercises in pairs or small groups c. Presenting to different audiences d. Body language e. Languageand pace f. How to use your audience as an asset g. How to interact with your audience h. How to remember yourpresentation i. Give and receive feedback on presentations j. Deal with nervousness and stay focused on yourpresentation

Teaching and learning activities : Lectures, written assignments, workshops, coaching, filming, group work, andpractical exercises in groups and with a learning peer.

Examination : Formative assessment during active participation in all parts of the course Summative assessmentof a. Poster presentation including scientific poster, b. Power Point presentation c. Elevator pitch

Compulsory elements : Three complete presentations (designed and presented to the class): a. Posterpresentation including a scientific poster b. Power Point presentation c. Elevator Pitch d. Giving feed back on theother students' presentations e. Reflecting on own learning and development during the course



More information : Welcome to apply for the doctoral course Present your research! The course will be given incentral Stockholm, in Gamla Brogatan (close to Hötorget). Please address all questions to:[email protected] or phone: 0707890607

Course responsible : Kristina Gemzell


[email protected]



[email protected]

















[email protected]



[email protected]

Title : Cellbased heart regeneration



Level : Doctoral level Responsible KI department : Department of Medicine, Huddinge

Specific entry requirements : Purpose of the course : This course provides tools and insights in regenerative medicine for heart disease.

Learning outcomes : Upon completion of the course, the doctoral students will be able to describe importantprinciples in studying the development of the human heart, relate these to heart disease, and critically evaluateimportant methods and technologies applied in the context of regenerative medicine for heart disease.

Contents of the course : The developmental principles, logic, pathways, technology, and model systems tounravel human heart disease. Regenerative cardiology, bioartificial heart tissues and translational bench to bedsideregenerative medicine.

Teaching and learning activities : The learning modes used in the course include lectures, discussions, seminarsand a one day research symposium.

Examination : The students are examined with individual and group presentations on the course themes. Compulsory elements : Participation in the group discussions and student presentations is mandatory.

Compensation is according to the instructions of the course director. Number of students : 12 20


More information :

Course responsible : Emil Hansson

Department of Medicine, Huddinge

[email protected]

Contact person : Emil Hansson

Institutionen för medicin, Huddinge

[email protected]

Title : Principles of cellular metabolism




Specific entry requirements : Purpose of the course : The course is intended to give a solid theoretical foundation for studying cellular

metabolism from a physical, quantitative perspective, enabling the student to critically approach literature in thefield, and serving as a preparation for more specialized courses.

Learning outcomes : After completing the course, the student should understand the principles underlying theorganization of metabolic pathways in human cells; be able to critically evaluate literature and data on cellularmetabolism; understand current methods for measuring cellular metabolism; and have a solid foundation to enabledeeper study of metabolism independently.

Contents of the course : The fundamental organization of cellular metabolism; physical constraints onmetabolism; important building blocks of metabolic pathways and their properties; major metabolites in humancells; carbohydrate metabolism; amino acid metabolism; nucleotide metabolism; lipid metabolism (briefly);principles of enzyme catalysis and bioenergetics of metabolic pathways; genomic organization of enzymes;properties of metabolic networks; metabolic fluxes and flux balance analysis; catabolism during nutrient starvation;anabolism in proliferating cells; methods for measuring metabolism, in particular isotope tracing; experimentalconsiderations when studying metabolism in cell systems.

Teaching and learning activities : The course will utilize a problembased learning model with "flippedclassroom" techniques, interactive seminars, problemsolving in groups, oral presentations, and individualassignments. Computer labs are included to study metabolic networks and metabolic flux analysis.

Examination : Knowledge is assessed by performance in connection to seminars (comments, questions, answers),performance on computer labs, and an individual home assignment (problem solving / essay) with a shortindividual oral presentation.

Compulsory elements : Presence on seminars and computer labs is mandatory. Absence must be compensatedfor by a written resume.



More information : The course will run at half speed, distributed over two weeks. The course includes own studytime (video lectures) and five half day seminars.

Course responsible : Roland Nilsson


[email protected]

Contact person :

Title : Kvalitetssäkring av klinisk forskning



Level : Forskarnivå Responsible KI department : Department of Medicine, Solna

Specific entry requirements : Purpose of the course : Kursen ger deltagaren kunskap och förståelse för vad som krävs för att kvalitetssäkra

klinisk forskning. Du kommer efter kursen veta hur man ska göra för att säkert och i enlighet med lokala ochnationella regelverk, etiska riktlinjer och internationella överenskommelser genomför klinisk forskning. Kursen äranvändbar för dem som arbetar med translationell eller klinisk laboratorieforskning. Den är också värdefull förforskare som arbetar med kvalitetsregister i vården, annan registerforskning och epidemiologisk forskning. Särskiltstort värde har kursen för de forskare som arbetar med interventioner av olika slag som medicinsk teknik ellerkliniska prövningar. Utöver den kompetens kursen ger dig kommer du att kunna avlägga test för erhållande av ettinternationellt gångbart certifikat i ICHGCP (International Conference on Harmonisation Good Clinical Practice).Oavsett forskningsområde kommer du förstå vikten av att sätta patientens säkerhet främst, och hur man gör föratt skapa säkra data som andra kan lita på.

Learning outcomes : Kunskap och förståelse Ha kunskap om hur man dokumenterar data så att samtligamoment i en klinisk forskningsprocess kan återskapas på ett tillförlitligt sätt Förstå innebörden avHelsingforsdeklarationen och Good Clinical Practice så att forskningspersoners autonomi och integritet alltid sätts iförsta rummet Ha kännedom om nationell, europeisk och internationell lagstiftning, vilka projekt som kräveransökan till olika myndigheter och hur detta går till Färdighet och förmåga Ha förmåga att avgöra vilka olikaansvar som prövare, medarbetare och sponsor har i en klinisk prövning Ha förmåga att sammanfatta ettprojektförslag i en synopsis och utifrån detta göra en riskanalys över ett projekt Visa färdighet i att användaenklare statistiska metoder för att avgöra ett projekts vetenskapliga validitet Värderingsförmåga ochförhållningssätt Kunna värdera forskningsprojektförslag utifrån patientens perspektiv med ett etiskt ochvetenskapligt förhållningssätt Visa förmåga att värdera information från olika källor framförallt databaser påinternet

Contents of the course : Kursen ger kunskaper om forskningsetik och hur ansökan till olika myndigheter görs,kunskap om kliniska prövningar, utveckling av nya behandlingar och då särskilt läkemedel, säkerhetsrapporteringtill myndigheter, personuppgiftslagen, etikprövningslagen, biobankslagen och patientdatalagen, arkivering,internationella register över kliniska prövningar, riskanalys och viss statistik

Teaching and learning activities : Kursen är en distansutbildning. Den omfattar två huvudspår som delvis gårparallellt. Det ena utgör arbete i grupp kring olika arbetsuppgifter som redovisas. Det andra utgörs av inläsning avGCPregler. Pedagogiken baseras flipped classroom som innebär att läsanvisningar ges tidigt och att studentendärefter individuellt och i grupp arbetar med olika problem, fall och case. Förslag på lösningar presenteras ochdiskuteras under lärarhandledning. Frågestunder erbjuds under kursen. Inläsningen stöds av frågor som studentenkan använda för att kontrollera sin egen inlärning. Enstaka föreläsningar som webinars kan komma att ges,beroende på den enskilda kursens behov.

Examination : Utöver ett godkänt grupparbete kommer det att ges en individuell examination med flervalsfrågor. Compulsory elements : Varje student måste delta i godkänt grupparbete. Varje student måste visa aktivitet på

kursens hemsida i form av minst fem frågor, presentationer och/eller kommentarer på andras inlägg. Frånvaro ellerbrist på online aktivitet kan efter examinators bedömning kompenseras med en individuellt skriven uppsats.


motivering), 2) datum för doktorandregistrering (där tidigare registreringsdatum har förtur) More information : Kursen är en lärarledd distanskurs som ger tillfälle till GCPprov efter godkänd examination.

Den kräver att studenten har tillgång till dator och nätverk.

Course responsible : Pierre Lafolie

Department of Medicine, Solna 0851779647

[email protected]

Klinisk farmakologi L7:05 Solna

171 76 Stockholm

Contact person :

Title : Quality assurance of clinical research




Specific entry requirements : Purpose of the course : This course provides the participant with the knowledge needed to secure the quality in

clinical research. It gives an understanding of what is required to act safely and in accordance with local andnational legislation, ethical guidelines and international treaty's when involved in clinical research. The course isuseful for those working with translational or clinical laboratory research. It is valuable for researchers working withpatient quality registries, other types of health registries and in epidemiology. It gives great value to researchersconcerned with interventional studies including medicinal products, surgical treatments or pharmaceuticaltreatments. Beyond the competence you will get, you can also take a test for an internationally recognizedcertificate in ICHGCP (International Conference of Harmonisation Good Clinical Practice). Regardless of yourresearch area, you will after this course understand how to protect patient's safety, and how to create trustful data.

Learning outcomes : Knowledge and understanding Knowledge on how to document data so all moments in aclinical research process can be recreated in a secured way Understand the meaning of the Helsinki Decaration andGood Clinical Practice so that research subjects autonomy and integrity always remain the first priority Knowledgeon Swedish, European and international legislations, on which projects that need to be applied for and to whichauthority, and how such applications are done Skills and abilities Able to decide what different responsabilities theinvestigator, study team members and sponsor has in the clinical trial Able to summarise a project proposal into asynopsis and based on that make a riskbenefit analysis of the project Able to use simple statistical tools to judgea project proposal's scientific validity Judgement and approach Able to judge project proposals from the patientperspective including a scientific and sound ethical approach Able to evaluate information from different internetdatabase sources

Contents of the course : The course provides insights into research ethics, and how applications to differentauthorities are done, it presents how clinical trials are undertaken, and how development of new treatments, inparticular medicinal products, are done, and how safety reporting to authorities is done. The following laws,regulations and sources are discussed: Act on integrity of personal data, Act on ethical review of research projects,Act on biobanking, Act on patient data in health care, Act on archiving, and international registry's on clinicalresearch. Risk analysis and some statistics are discussed.

Teaching and learning activities : The course is based on elearning. There are two tracks, in part parallel. Onetrack is based on group work around cases that are presented to the course. The other track is based on individualstudies of GCP regulations. Both tracks include study material and tutor support. The pedagogy is based on flippedclassroom meaning that instructions and learning resources will be made available early to support the individuallearning and group works. Cases and their solutions will be presented and discussed under teachers supervision.Q&A will be provided. The GCP studies will be supported by MC self tests. Webinars may be provided, pending theneed from the course.

Examination : In addition to an approved group work there will be an individual multiple choice examination. Compulsory elements : Each student must participate in a group work. Each student must show activity on the

course's home page with at least five questions, presentation and/or comments on others postings. Absence or lackof online activity can after the examiner's assessment be compensated by an individually written essay.



More information : This is a tutorled elearning providing a GCPtest after approved examination. The studentneed access to internet and a computer to be able to participate.

Course responsible : Pierre Lafolie

Department of Medicine, Solna 0851779647

[email protected]

Klinisk farmakologi L7:05 Solna

171 76 Stockholm

Contact person :

Title : Practical approach to animal models in cardiovascularresearch




Specific entry requirements : Laboratory animal science course equivalent to a FELASA B or FELASA C level(Directive Function A, D EU Directive 2010/63 art. 2326). Researchers with education in laboratory animalscience from countries other than Sweden need to pass the Swedish legislation, ethics and animal use coursebefore they will be granted access to animal facilities at Karolinska Institutet.

Purpose of the course : The purpose of the course is to enable doctoral students to obtain practical experience inmodels of cardiovascular research as well as to discuss with fellow students and experts in the field the theory ofthe models and ethical aspects of translation research.

Learning outcomes : At the end of the course the participant should be able to: Know how to develop, andmaintain breeding programs for genetically manipulated mice in the most optimal fashion Show an understandingon how to maintain experimental mice in order to investigate cardiovascular diseases and obtain maximal data fromeach experiment Show an understanding of the main functional cardiovascular disease models and how to usethem Understand the benefits and limitations of the cardiovascular disease models that are used Be able topractically perform common mouse models for cardiovascular disease

Contents of the course : The course is aimed at students who are starting or have just started to use animalmodels in cardiovascular research. It is designed for students who have done a basic animal course such as FELASAB or C. The course will give theoretical knowledge about how to create genetically manipulated mice, as well asbreeding and maintaining mice for optimal use. Furthermore, an incite to other animal models will be given such aspigs and rats. There is also a practical component where students will get handsonexperience in the mostcommon models used.

Teaching and learning activities : The course is partly theoretical, partly practical, where lectures/groupdiscussions and laboratory demonstrations are integrated. Time is also allocated for discussing of laboratory resultsand lectures.

Examination : All the learning outcomes of the course have to be reached to pass the course. The final grade(pass or fail) will be based on: summative assessment of the contributions during the discussions that are part ofthe course individual presentation at a seminar where different aspects of an animal model will be discussed, i.e.disease aspect to be investigated, which model would suit best, and how are the results analyzed and interpreted

Compulsory elements : Practical sessions are compulsory. Absence from practical sessions cannot becompensated for, but absence from one theoretical session can be compensated for in subsequent sessions.



More information : This course will have a large practical component working with animal models, thereforestudents must have completed FELASA B and have been approved into a KI animal house facility.

Course responsible : Lars Maegdefessel


[email protected]

Contact person : Alexandra Bäcklund Institutionen för medicin, Solna

[email protected]

Title : Current advances in atherosclerosis research




Specific entry requirements : Participants should have a basic knowledge of atherosclerosis. Purpose of the course : This course will provide an historical and contemporary overview of the major discoveries

in atherosclerosis research. The course is specially planned to support the PhD students in the area ofcardiovascular research by giving them an opportunity to deepen their understanding of the molecular mechanismsinvolved in atherosclerosis.

Learning outcomes : At the end of the course the participant should be able to: Recognize the majorbreakthroughs that led to atherosclerosis being seen as a chronic inflammatory disease rather than a mere lipiddisorder. Present and discuss these findings in the form of a seminar. Critically evaluate research papers insmall groups. Hypothesize new therapeutic opportunities for the treatment of cardiovascular disease.

Contents of the course : 1 Atherosclerosis as an immune disease: Major clinical and experimental findingssupporting this notion. 2 Possible approaches to investigate atherosclerosis. 3 The role of the immune system inatherosclerosis. 4 Antiinflammatory therapies for cardiovascular disease. 5 Hot topics in atherosclerosis.

Teaching and learning activities : The course consists of 10 halfday sessions: 5 sessions (study time) will beused by the students to prepare for the seminars (5). During each seminar one or several specific aspects ofresearch in atherosclerosis will be studied. A typical structure for a seminar involves: An introduction about thetopicofinterest by an invited expert. Presenting, analyzing and discussing an assigned paper following a journalclub style where everyone is expected to participate.

Examination : Formative assessments will be conducted throughout the seminars. All the intended learningoutcomes will be assessed. To pass the course, a participant has to: Actively participate in the discussions duringthe seminars. Present a selected publication relevant to the subject (working in small groups). Demonstrate atrue understanding of research perspectives of atherosclerosis.

Compulsory elements : All group discussions are compulsory Number of students : 8 25


More information : The course activities (5 seminars) will take place at KI Solna Campus between March 8 andApril 27.

Course responsible : Andres Laguna Fernandez Department of Medicine, Solna

[email protected]

Contact person :

Title : Principles of toxicology




Specific entry requirements : Purpose of the course : The purpose of the course is to learn how chemical substances can have

unwanted/adverse effects on living organisms and how the toxicity is studied. Learning outcomes : Upon completion of the course, the student should be able to: describe the principles of

toxicology explain how toxicological methods are applied evaluate toxicological data reflect on the role oftoxicology in biomedical research and for sustainable development

Contents of the course : Toxicology is the study of unwanted/adverse effects of chemical substances on livingorganisms. Toxicology deals with substances such as pharmaceuticals, environmental pollutants, chemicals incosmetics, clothing or other everyday products and pesticide residues, food additives and other substances in food. The course introduces the history of toxicology and the tasks and scope of toxicology today in biomedical researchand for a sustainable society. It moves on to the general principles of toxicology, including exposure to chemicals,absorption, distribution and elimination of chemicals, toxic effects on different organs and the role of doseresponserelationships. Thereafter the application of in vivo, in vitro and in silico toxicological methods is discussed. Ethicalprinciples of toxicological studies are addressed. Toxicological data from different methods is analysed usingexamples from toxicological research studies. The participants will discuss how their own research questions canrelate to toxicological research.

Teaching and learning activities : Teaching and learning activities include lectures, exercises and groupassignments.

Examination : Examination is in the form of a written assignment and/or oral presentation. Compulsory elements : Participation in the exercises and group assignments is compulsory. Absence can be

compensated with an individual task. Number of students : 8 30


More information :

Course responsible : Charlotte Nilsson


[email protected]


[email protected]

Nobels väg 13

17177

Stockholm

Title : Regenerative Medicine: Principles to Practice




Specific entry requirements : None. Purpose of the course : The overall purpose of the course is to expose students to the latest scientific findings in

the field of regenerative medicine, and to provide students with skills to conceptually develop independent lines ofresearch within collaborative international networks.

Learning outcomes : After completion of this course, the student will be able to describe the basics of stem cellbiology and provide an appreciation for novel approaches and applications in regenerative medicine. The studentwill be able to demonstrate an interdisciplinary understanding of central concepts in stem cells and criticallyevaluate the potential, advantages and drawbacks of different methods that are currently researched in the fields ofstem cell and regenerative therapy. The student will be able to extract and integrate information from stateoftheart lectures, scientific articles and literature search within the field.

Contents of the course : The course covers principles of stem cell biology and provides an appreciation forapplications in regenerative medicine. Lectures and journal clubbased topics include fundamental features of stemcell platforms, as well as the use of these and other platforms in the design and development of regenerativetherapies. The course will exemplify how regenerative therapies can be targeted to different organs (e.g. within thecardiovascular system and the nervous system) with particular emphasis on the stateoftheart technologies,prospects for clinical translation and current challenges within the field. The student will be required to take anactive part in this course by contributing in journal clubs and discussions related to stem cellbased regenerativemedicine.

Teaching and learning activities : The pedagogic frame of this course is based on lectures combined with topicrelated research articles. Approximately half of the lectures will take place at KI (Huddinge and Solna campus). Theother lectures will take place at Mayo Clinic and will be projected to students at KI via video conferencing. Thecourse includes journal clubs where the students are required to present articles (written and orally), integrate theknowledge acquired from lectures and reading of the articles, and actively discuss their acquired knowledge as agroup. Some journal clubs will be carried out in groups using interactive eplatforms. The examination task consistsof a written report that is handed in for evaluation toward or at the completion of the course.

Examination : The examination consists of a written report that is handed in for evaluation at the end of thecourse. All students are also required to peerreview another student's examination report. The individualperformance of each student will be evaluated separately.

Compulsory elements : Active participation in lectures and journal clubbased discussions is mandatory.Compensation according to the instructions of the course director.



More information : The course will be held on Wednesdays 15.0017.00. About half the sessions will take place inthe Solna campus and half the sessions in the Huddinge campus.

Course responsible : Natalia Landazuri


[email protected]

Contact person : Natalia Landazuri

Institutionen för medicin, Solna

[email protected]

Title : Core concepts in global health and global burden of disease




Specific entry requirements : Ingen Purpose of the course : The purpose of the course is to provide students with a broad perspective on global

health and the range of solutions to critical health issues; students will also develop their skills in critical analysis,and will develop confidence in building and presenting arguments in favor of or against various solutions toaddressing health issues at a global level.

Learning outcomes : Describe broad trends and inequality in the burden of disease in low, middle and highincome countries; Discuss globalization and the drivers of these trends; Understand how data on the globalburden of disease is collected and analysed; Describe key actors, intuitions and legal regimes in global health; Discuss challenges in implementing the healthrelated Sustainable Development Goals; Discuss the role of healthsystems in addressing current global health challenges

Contents of the course : Trends in the global burden of disease, including infectious disease, noncommunicabledisease, mental health, accidents and violence; Drivers of global inequalities in health; Challenges in measuringand analysing the global burden of disease; including a critical review of indicators and measurement platforms Global health governance and financing; Service delivery, health systems and concepts of quality of care The legalbasis underpinning action in global health; Development theories and the role of culture in global health Historicalreview of key approaches and strategies, initiatives and international agendas in global health including maternal,reproductive and child health, HIV, malaria, rational drug use/drug resistance in health and beyond, humanitarianaid Implementation of Sustainable Development Goals for health, particularly Goal 3; Current challenges in globalhealth, such as migration, climate change and Ebola.

Teaching and learning activities : The course is structured through a combination of lectures, group work andselfdirected learning in order to provide students with the tools to be analytical and reflective about how their ownPhD topics fit into the wider context of global health.

Examination : The examination consists of an oral and a written essay part. Both needs to be passed to get a passgrade for the course. The students need to show by way of the discussions that they have obtained a broadunderstanding of core concepts in global health and global burden of disease. Students should present on the lastday of the course an outline of an essay reviewing and reflecting on how their research addresses global health anddevelopment. Students will be asked to write an approximatly 2000 words essay on their research topicsummarising linkages to the global context. Students should review and reflect on how their research addressesglobal health and development by summarising the learning from this course and applying it to their research topic.The essay is a takehome exam and is due five working days after the end of the course. The course grade ispass/fail.

Compulsory elements : Number of students : 10 20


More information : The course will run as a fulltime course over one week with a combination of lectures, groupwork and selfdirected learning.

Course responsible : Claudia Hanson

Department of Public Health Sciences

[email protected]

Contact person : Claudia Hanson

Institutionen för folkhälsovetenskap

[email protected]

Title : Heart failure from pathophysiology to evidence basedtreatment




Specific entry requirements : undergraduate study in medicine or biomedicine Purpose of the course : To provide a comprehensive overview of heart failure, a major public health problem and

the most common cause of hospitalisation. The course will address all aspects of the disease, from mechanism andpathophysiology, to how these aspects affect diagnosis and therapeutic effects. The course will also introduce thenew developments and future directions of heart failure research.

Learning outcomes : To be able to define and understand heart failure and its different phenotypes; to be able tounderstand the pathophysiological basis for diagnosis and therapy; to be able to understand and account forconcepts for developing and testing novel interventions; and to demonstrate a good understanding of translationalapproach between basic research and the development of treatment of heart failure, as well as the principles ofregistry based research on heart failure.

Contents of the course : The module will cover pathophysiology, clinical diagnosis and treatments, as well asepidemiology of heart failure. A series of lectures will be given to reveal the molecular and cellular mechanisms ofheart failure development, the relations of heart failure to other cardiovascular diseases, and new diagnotic andtherapeutic approaches of the disease. Registry based research of heart failure will also be addressed.

Teaching and learning activities : The 2day course module includes course lectures and seminars. Examination : Written exam.

Compulsory elements : The participants must attend the lectures and seminars. The students who have missedthese sessions can book extra session time within 4 weeks to compensate the absence.



More information : Two full days. Tuesday 13th of March and Tuesday 20th of March 2018.

Course responsible : Tonje Thorvaldsen


[email protected]

Contact person : Lars Lund

Institutionen för medicin, Solna

[email protected]

Nailin Li Institutionen för medicin, Solna

0851773996 [email protected]

Clinical Pharmacology Unit Karolinska University HospitalSolna

17176 Stockholm

Title : Manuscript writing in English



Level : Doctoral level Responsible KI department : Department of Clinical Science and Education, Södersjukhuset

Specific entry requirements : Purpose of the course : The purpose of this course is to increase the competence and efficiency of the doctoral

students in academic writing with a focus on writing scientific manuscripts. The ability to publish in high qualityscientific journals is crucial for a successful completion of the doctoral education and pursuing a career that requiresa PhD. Participation in this course is thus likely to benefit the students in both short and longterm perspective.

Learning outcomes : After completing the course the students should be able to: (1) prepare for writing amanuscript and choose an approach to write the manuscript, (2) compose the first draft consisting of the standardstructures, (3) choose and use tables, figures, graphs, photographs, and schematic diagrams appropriately, (4)revise the first (and subsequent) drafts for clarity, brevity, coherence and readability, (5) improve choices of words,and styles of sentence constructions, (6) write grammatically correct texts, punctuations, numbers as numbers,and numbers as words, (7) submit a manuscript, address the comments from the referees, and resubmit themanuscript. Contents of the course : The process approach of writing; literature review; plagiarism, ethical issues,permissions, and authorship issues; choice of journals; how to write the different parts e.g. introduction, materialsand methods, results, discussion, conclusion, acknowledgement, references, abstract, and title of a manuscript;tables, figures, graphs; statistics; tense, spelling and grammar; readability, clarity and brevity; abbreviations andacronyms; numbers as numbers, and numbers as words; choice of words, active and passive voices; which andthat; subject verb agreement, correct placement of modifiers, punctuations, capitalizations; submission format,common mistakes in grammar and choice of words; how to reply to the comments of the referees, revise andresubmit; practical tips; how to overcome writers´ block.

Teaching and learning activities : We shall use the concepts of active learning, flipped classroom, deliberatepractice, and formative and summative assessments as the main methods for teaching and learning in this course.Instead of traditional lectures, there will be smallgroup interactive learning sessions, interspersed with probingquestions, tasks, groupworks, and individual studies. Students will solve problems and perform writing tasks thatare constructed by the teachers, with welldefined learning objectives. Students will receive accurate andimmediate feedback from the peers and the teacher to facilitate learning. During the course, students will write partof their own manuscript under the supervision of the teacher.

Examination : Participants will write part of their own manuscript (approximately 2000 words) where they willincorporate the newly acquired knowledge from the course. Compulsory elements : Presence in all of the scheduled sessions and participation in the writing tasks areobligatory. Absence should be compensated for in accordance with the indications of the course director.



More information : The course will be given at the Department of Clinical Science and Education, Södersjukhuset,from 09:00 16:00 everyday from Monday to Friday. You can reach Södersjukhuset by metro (nearest metrostation Skanstull) or by bus number 3.

Course responsible : Shahidul Islam

Department of Clinical Science and Education, Södersjukhuset 086163950

[email protected]

Contact person :

Title : Public Health Research concepts and theories




Specific entry requirements : Purpose of the course : This course is designed for students in all areas related to advancing the health of the

population or who want an understanding of the theories and concepts relevant when doing public health research.After this course the student should be able to put her/his research in a public health context and relate it to keypublic health concepts.

Learning outcomes : The learning outcomes are: 1. Discuss what constitutes a public health issue; 2. Reflectupon key public health concepts in relation to your own research area; 3. Discuss how theory can aid in advancingresearch in public health; 4. Reflect upon the role of political and social discourses on public health issues andhealth policies

Contents of the course : The course provides knowledge on key concepts and theories in the multidisciplinaryfield of public health and an overview of the development of public health as a research area. Areas that will becovered include the concept of health and how it may be measured, global health needs and priorities, healthpolicies, health prevention and promotion as well as determinants of health and health inequalities. Theories inthese areas as well as on social stratification, gender and intersectionality are explored.

Teaching and learning activities : Different strategies for teaching and learning will be used such as lectures,groupdiscussions, peer reviewing and article seminars. The focus will be on critically reflecting upon the knowledgeand relating it to your own research.

Examination : To pass the course the student has to achieve the learning outcomes and this will be assessed insmall group assignments and an individual assignment.

Compulsory elements : Group assignments, article seminars and seminar on individual assignment arecompulsory. If the student is unable to attend, a written report of the questions related must be handed in.



More information :

Course responsible : Sara Fritzell


[email protected]

Contact person : Janne Agerholm

Institutionen för folkhälsovetenskap

[email protected]

Title : Multi modality imaging in oncology



Level : Doctoral level Responsible KI department : Department of Molecular Medicine and Surgery

Specific entry requirements : Purpose of the course : To describe the various imaging modalities used in the field of oncology, how multi

modality imaging can be used to predict and assess treatment response and to describe how standardizedinterpretation of oncological imaging is performed in research, clinical trials and in individual patient care usingexisting standards such as PIRADS, RECIST, WHO and other criteria.

Learning outcomes : At the end of the course, the student is expected to (1) understand the basics of imagingmethods and multi modality assessment in oncological imaging, (2) understand advantages and limitations ofdifferent imaging techniques (3) describe how to use diagnostic imaging in an oncological research project plan

Contents of the course : This course covers both preclinical and clinical aspects of oncological imaging. Thestudent will be introduced to basic diagnostic modalities, cancer histopathology, molecular diagnostics and clinicalimplementations. Principle strategies for planning, performing and monitoring of cancer will be addressed. A finalgoal is that the students will be able to formulate a translational project of oncological imaging related to their ownresearch fields.

Teaching and learning activities : The course will include a series of learning activities, such as introductory andcomprehensive lectures/seminars, group discussions and casestudies.

Examination : The course assignment will consist on writing an individual short project (max 1 and ½ half page)where one or more imaging techniques learnt during the course should be applied to a research topic that intereststhe student. The project description should be handed in maximum three weeks after the completion of the courseto the organizers via email.

Compulsory elements : Attendance to all the activities of the course and the individual presentation of a researchproposal are mandatory. Absence from mandatory parts of the course will be compensated by other activities afterdiscussion with the course organisers.



More information : The course is a joint course with the National Clinical Oncology research school NatiON andwill be held at the Department of Diagnostic Radiology, Karolinska University Hospital, Solna. More information willbe provided to the students in due time, before the beginning of the course.

Course responsible : Chikako Suzuki

Department of Molecular Medicine and Surgery

[email protected]

Contact person :

Title : The epigenome: a platform for the integration of metabolicand signaling pathways in development and on the path to diseases



Level : Doctoral level Responsible KI department : Department of OncologyPathology

Specific entry requirements : Purpose of the course : To increase the understanding of the interplay between epigenetic regulation, signalling

and metabolic pathways in complex human diseases. Learning outcomes : Following the completion of the course the students will be able to describe and discuss the

basic principles of epigenetic regulation and the role of chromatin in the maintenance of cellular phenotypes.Moreover, the students will learn how various signaling and metabolic pathways alter chromatin states duringageing and in human diseases, such as cancer, diabetes and psychiatric disorders. The students will also be able todesign experiments for studying chromatin marks and to critically evaluate results obtained with these techniques.

Contents of the course : The course covers the molecular mechanisms of epigenetic regulation and howchromatin based processes are linked to human diseases. Particular attention will be paid to the crosstalk betweenchromatin marks and cellular signaling pathways as well as metabolism. Furthermore, we will discuss the regulationof these processes during the circadian cycle and their deregulation in cancer, diabetes mellitus and psychiatricdiseases.

Teaching and learning activities : The learning activities used in the course include lectures, research seminars,group discussions, problembased learning and research article presentations by the students. Every student willpresent a recent publication in the form of a journal club. Students will also be encouraged to actively participate inthe course. There will be substantial time for discussions after the lectures and research seminars.

Examination : Examination is based on the journal club presentation (summative assessment) and on activeparticipation in discussions during the course (formative assessment). Every student will be at one occasionpresenting a preselected article and at another occasion will be the opponent for the presentation of a fellowstudent. The student's performance at these two occasions will be the basis for the final assessment.

Compulsory elements : The lectures, seminars, group discussions and journal club presentations are compulsory.Number of students : 10 18


More information :

Course responsible : Anita Göndör

Department of OncologyPathology 08 524 862 03

[email protected]

Contact person : Matti Nikkola

Institutionen för cell och molekylärbiologi

[email protected]

Title : Principles of nucleic acid structure




Specific entry requirements : Purpose of the course : The purpose of the course is to provide participants a good and uptodate knowledge of

DNA and RNA structural biology, to stimulate the curiosity and to inspire their own research in the field such asRNA/DNA biology, biotechnology and DNA/RNA therapeutics. To deeply understand how molecules work, detailedknowledge of their structures is necessary. The course aims also to help to practice key academic skills, such aslearning from scientific presentations and literature, providing constructive criticism and presenting scientific data inoral/written form.

Learning outcomes : After the course, the students should be familiar with the principles regulating DNA/RNAstructures and with the techniques used to provide DNA/RNA structural information. Furthermore, the studentsshould have acquired the capacity to visualize three DNA/RNA dimensional structure and to identify the relationbetween structure and function

Contents of the course : A general introduction to nucleic acids nomenclature. Structural and conformationalfeatures of nucleotides. Physical properties. Hydrogen bonding and base stacking. Water and nucleic acid. Metal ionand nucleic acid. Secondary and tertiary structures of DNA and RNA and techniques to determine structures anddynamics of DNA and RNA systems (such as xray crystallography, NMR, theoretical approaches and so on) Generalconsideration on proteinnucleic acid interactions, DNA superhelix, higher order nucleic acid structure. Lastadvances in DNA/RNA structural field.

Teaching and learning activities : The course consists of lectures, computer tutorial, short presentations by thestudents and seminars from national and international experts. The participants are involved inclass (individualand group) activities. The students should integrate each lectures hour with homework.

Examination : Written exam, graphical and oral presentation on a selected topic Compulsory elements : The compulsory parts of the course are the lectures, computer tutorial and the seminars.

Absence will be compensated with extra assignments. The students will get some key questions on thecorresponding lecture topic, and the answers should be submit in written form for review and approval.



More information : The course starts with some individual activities during week 15. Lectures will be heldMondayFriday, from 9:00 to 16:00 at Flemingsberg campus during week 16 (16/420/4). Individual and smallgroup activities, symposium and tutorials will be held during week 17.

Course responsible : Alessandra Villa

Department of Biosciences and Nutrition +468524 81081

[email protected]

Hälsovägen 7 NOVUM

141 83 Huddingen

Contact person :

Alessandra Villa Institutionen för biovetenskaper och näringslära

+468524 81081 [email protected]

Hälsovägen 7

NOVUM 141 83 Huddingen

Title : Statistics with R from data to publication figure




Specific entry requirements : none Purpose of the course : Do you need to turn data into a publication figure? We offer tools and confidence for the

student to independently select a statistical method for research questions in their field. Furthermore we teach astructured way to discuss their choice efficiently with a professional statistician. The course is practical and includesimplementing a basic statistical analysis in R, the leading statistical programming language in bioinformatics andmedical science. Students can bring data from their own research project, or work on data from the course.

Learning outcomes : By the end of the course the student should be able to: * download and install the latestversions of R and Rstudio. *know where to look for help when working in R. *know how to import data into R. *useR for basic analysis and presentation of data in their field. *select statistical method and motivate the choice usinga structured approach. *communicate efficiently with a statistician about their choice of statistical method.

Contents of the course : Basics of R. Download, install, import data, basic analysis, how to get help. Learn tospeak statistics. A structured approach to selecting statistical method and communicating with a statistician. Practice how to go from data to publication figure using data from your project or more or less friendly data offeredby the course.

Teaching and learning activities : Distance learning with online lectures, quizzes and interaction with otherstudents. Campus lectures and computer work using your own computer. Individual project work.

Examination : Online examination. Participation in labwork and seminar. Written project work with executablecode.

Compulsory elements : Online quizzes and tasks. Active participation in online discussions (asynchronous, notbound to a particular time of day). Active participation in computer lab sessions. Written report includingexecutable code. Active attendance in seminar. Compulsory attendance approximately four afternoons and one day. Number of students : 20 30


More information : The course starts with a kickoff meeting April 25 at 09301200 helping you to get started withthe distance learning part of the course. The distance learning is at your own pace, but should be finished by May13. For the novice, the distance learning corresponds to one week full time studies. May 14 through 18 arescheduled full days with lectures, work shop, preparation time and poster presentations. All scheduled activitiestake place in Huddinge.

Course responsible : Andreas Montelius


[email protected]

Karolinska University Hospital

14186 Stockholm

Contact person :

Eva Hagel Institutionen för lärande, informatik, management och etik

[email protected]

Title : Neural Control of Inflammation: An introduction toBioelectronic Medicine




Specific entry requirements : Purpose of the course : The purpose of this course is to give doctoral students insights into the neural control of

homeostasis, particularly the regulation of inflammation, and how engineering, neuroscience, immunology andclinical medicine can come together to find new ways to treat disease.

Learning outcomes : After the course, the doctoral student will be able to define prototypical neural circuits thatregulate homeostasis explain the role of inflammation in the pathogenesis of and recovery from autoimmunediseases, cardiovascular diseases and infection identify the components of the "inflammatory reflex" discussregulatory mechanisms for cytokine release classify different interfaces with the nervous system and the immunesystem contrast advantages and drawbacks with major treatment approaches for inflammatory diseases describemolecular sensors for danger in the immune system and the nervous system define bioelectronic medicine andexplain its potential role in clinical medicine summarize challenges in engineering and medicine for development ofbioelectronic medicine technology

Contents of the course : Neural control of organ systems will be discussed in molecular, cellular and clinicalperspectives. Special attention will be given to the mechanisms that detect and regulate inflammation. Theneurophysiology of vagus nerve stimulation and other treatments that involve interfacing with the nervous systemwill be reviewed. Progress in neural interfacing and device development within the emerging field of BioelectronicMedicine will be discussed.

Teaching and learning activities : Lectures, a student project group and a student presentation. Examination : Project presentation and written examination.

Compulsory elements : Lectures, project group participation, active participation in presentation and passing theexamination is compulsory for "PASS". Limited absence from lectures can be compensated for after individualdiscussion with the course organizers.



More information :

Course responsible : Peder Olofsson


[email protected]

Contact person :

Title : Introduction to R




Specific entry requirements : Biostatistics I: Introduction for epidemiologists or corresponding courses. Purpose of the course : The purpose of this course is to introduce students to using the R statistical software to

perform basic to intermediate statistical data analysis in a replicable manner. Learning outcomes : After successfully completing this course, students are expected to be able to: explain

basic concepts of the R language and environment, the online and offline sources of documentation for R, andbasic concepts of data management and workflow in a standard statistical analysis, run a standard statisticalanalysis interactively within the R environment, formalize and document such a standard analysis as a standalone R script, produce graphical representations, as part of reporting their analysis, interpret their scripts forpotential simplifications via functional implementation, find, install and compare extension packages for unfamiliarstatistical applications.

Contents of the course : The course will cover the basic elements of a standard statistical workflow: reading datainto R; preprocessing and quality assessment of data via numerical and graphical methods; descriptive statisticsvia summary measures, tabulations and graphics; basic statistical inference in terms of significance testing andconfidence intervals; specification, fitting & diagnosis of regression models; exporting and reporting results fromthe previous steps. The course includes an introduction to the Rstudio integrated development environment toprovide a common framework for interactive and scripted analysis. The extensibility of the R system will bedemonstrated by example.

Teaching and learning activities : Course days will be organized around a common theme, with concepts andbackground covered in the mornings via presentations, demos, inclass exercises and discussions, and practicalapplication via individual and smallgroup lab exercises in the afternoons. Formative assessment will be integratedvia inclass quizzes and lab reviews.

Examination : Students will perform an openbook examination based on practical application of the conceptspresented during the course to realistic data sets and problems. Students who do not pass the examination will beoffered a second examination within two months from the end of the course (excluding academic holidays).

Compulsory elements : The individual examination (summative assessment) is compulsory. Number of students : 8 25


More information :

Course responsible : Alexander Ploner

Department of Medical Epidemiology and Biostatistics 0852482329

[email protected]



Title : Fundamentals of statistical modeling




Specific entry requirements : Courses "Epidemiology I: Introduction to epidemiology", "Epidemiology II: Designof epidemiological studies", "Biostatistics I: Introduction for epidemiologists", "Biostatistics II: Logistic regressionfor epidemiologists" and "Biostatistics III: Survival analysis for epidemiologists"or corresponding courses.

Purpose of the course : The purpose of this advanced course is to provide an introduction to the tools ofstatistical modeling.

Learning outcomes : After successfully completing this course the students should be able to do the followingindependently of others: explain the concepts of marginal and conditional distributions, illustrate the relationshipbetween cumulative distribution, probability mass/density, quantile, sparsity, cumulative hazard, and hazardfunctions, propose possible models for the above functions both marginally and conditionally on covariates, identify suitable models to answer scientific research questions and motivate the choice, estimate the parametersof the above functions, and use standard statistical software, evaluate the fit of the model, and critically interpretthe results.

Contents of the course : The students are introduced to a general framework for data analyses that hinges oncreating statistical models. The course focuses on the intricacies and potentials of modeling in a number ofexamples and realdata applications. The range of the covered examples is broad, and some examples are workedout in greater details than others. The course will enable students to gain an advanced knowledge of (1) randomvariables, (2) joint and conditional probability distributions, (3) modeling tools, (4) interpretation of statisticalmodels, (5) relations between known methods, (6) estimation tools, (7) computer programming. The students willimprove the level of knowledge of the foundations for data analysis, statistical practice, and use of statisticalsoftware. They will also be prepared to pursue more advanced studies in statistics. The focus of the course is onanalysis of real data and interpretation.

Teaching and learning activities : The course activities are based on lectures and computer exercises, exercisesnot requiring statistical software, and literature review. We will provide laptop computers to all participants, butparticipants are welcome to bring their laptops if they prefer.

Examination : Individual written examination based on practical application of the course content, where thestudent has to show that all the intended learning outcomes have been achieved. Students who do not pass theexamination will be offered a second examination within two months from the end of the course.



More information : The individual examination will be performed as a takehome examination.

Course responsible : Matteo Bottai

The institute of Environmental Medicine 08524 870 24

[email protected]


[email protected]

Nobels väg 13

17177

Stockholm

Title : Open science and reproducible research




Specific entry requirements : Purpose of the course : The purpose of the course is to provide an overview of current challenges in

reproducibility and to provide tools and skills for students wishing to practice science openly. Learning outcomes : After the course, students should be able to: Analyse reproducibility problems in science,

including the impact of analysis flexibility and questionable research practices, and identify practices contributing toimproved reproducibility Account for principles of replication research Preregister research protocols and assessothers' preregistered research protocols Openly publish scientific works including data and code, and find andmake use of scientific works, including data and code, published by others.

Contents of the course : The "reproducibility crisis" in biomedical sciences: what is it? Research fraud andquestionable research practices Impact of bias due to analysis flexibility Observed statistical power andimplications for inference Comprehensive methods reporting and fieldspecific guidelines Preregistration ofprotocols Replication research Open access publishing Open materials, open data, and open code Introduction to principles of data reuse in secondary analyses and metaanalyses

Teaching and learning activities : The course will contain lectures, seminars, workshops, and a final assignment.The purpose of the lectures is to introduce the concepts covered by the course and to situate them in context. Theseminars will cover the course literature, which the students will be expected to critically appraise. Computerassisted workshops will be used as interactive learning activities to cover some parts of the course, e.g. statisticalpower.

Examination : Examination consists of an assignment where students will be able to choose a topic related to thecourse content, and write a short report. For example, they may compare a preregistered protocol to the publishedscientific paper, or they may attempt to replicate results from a published paper using openly published data. Thisassignment will be presented before the class and students will give comments on each others' presentations.

Compulsory elements : Participation in the seminars and labs is mandatory. Absence from a seminar may becompensated by writing a short reflection paper on the literature for that seminar. Participation in the finalassignment presentation session is also mandatory.



More information : The course will be held at Campus Solna. Materials from when the course was given in thespring of 2017 are available here: https://osf.io/fa9rg/. The course is given jointly by the doctoral programmes inNeuroscience and Cell biology and genetics. See: http://ki.se/medarbetare/forskarutbildningsprogram.

Course responsible : Gustav Nilsonne


[email protected]

Contact person :

Title : Medical research ethics




Specific entry requirements : Purpose of the course : The objective of this course is to provide the doctoral student with tools to deepen his or

her knowledge of medical research ethics and good research practice; and to enhance the doctoral student's abilityto critically discuss and reflect upon ethical questions that can derive from research. This is to provide the doctoralstudent with enhanced possibilities to reflect on ethical aspects of his or her own research.

Learning outcomes : After having completed the course, the doctoral student should: be able to give anaccount of important research ethical theories and principles. be able to identify, analyze and discuss ethicalproblems in research on humans and animals have an ethical approach to research

Contents of the course : The course includes the following: Important research ethical theories and principles. Ethical guidelines on how to conduct research, such as the Helsinki Declaration. Cases that are problematicfrom an ethical point of view. Ethical aspects concerning research on humans. Informed consent and its ethicalbasis. Ethical aspects concerning research on animals, including arguments for and against using animals forresearch purposes, as well as the three R:s. Deviations from good research practice, fraud, fabricated data andplagiarism Handling of authorship in scientific writing Conflicts of interest in research Ethical review Important concepts and positions in philosophy of science, and connections between philosophy of science andresearch ethics

Teaching and learning activities : Lectures, group work and general discussions. Examination : The doctoral student writes an essay on a research ethical theme, in relation to all intended

learning outcomes, preferably related to his or her own research. A small number of students get the opportunity toorally present an ethical reflection concerning their research in front of the whole group.

Compulsory elements : Attendance is mandatory for the group work and general discussions. If the student isabsent, he or she can to some extent compensate by handing in written answers concerning the cases that havebeen discussed.


earlier registration date), 2) the relevance of the course syllabus for the applicant's doctoral project (according towritten motivation).

More information :

Course responsible : Gert Helgesson


[email protected]

Contact person : Annelie Jonsson


[email protected]














More information :



[email protected]



[email protected]

Title : Medicinsk forskningsetik



Level : Forskarnivå Responsible KI department : Department of Learning, Informatics, Management and Ethics

Specific entry requirements : Purpose of the course : Syftet med kursen är att fördjupa den forskarstuderandes förståelse för medicinsk

forskningsetik och god forskningssed; samt att förbättra den studerandes förmåga att kritiskt reflektera ochargumentera kring etiska problem som kan uppstå i samband med forskning. Detta i syfte att ge denforskarstuderande förbättrade möjligheter att reflektera kring etiska aspekter av den egna forskningen.

Learning outcomes : Den forskarstuderande ska efter avslutad kurs: kunna redogöra för centralaforskningsetiska teorier och principer. kunna identifiera, analysera och diskutera etiska problem som kan uppstå isamband med forskning på människor och djur. ha ett forskningsetiskt förhållningssätt.

Contents of the course : Kursen innehåller följande moment: Centrala forskningsetiska teorier och principer. Forskningsetiska riktlinjer, t ex Nürnbergkoden och Helsingforsdeklarationen. Forskningsetiskt problematiska fall. Etiska aspekter på forskning på människor. Informerat samtycke och dess etiska grund. Etiska aspekter pådjurförsök, innefattande argument för och mot att använda djur för forskningsändamål, samt "de tre R:en". Avvikelser från god forskningssed, fusk, fabricerade data och plagiat. Hantering av vetenskapligt författarskap(medförfattarskap, författarordning). Intressekonflikter i forskningen. Etikprövning. Centralavetenskapsteoretiska begrepp och positioner, och dess relevans för forskningsetik.

Teaching and learning activities : Föreläsningar, grupparbeten och plenumdiskussioner. Examination : Deltagaren genomför en skriftlig forskningsetisk reflektion företrädesvis angående det egna

forskningsprojektet. Ett fåtal studenter ges möjlighet att muntligt redovisa en forskningsetisk reflektion, i relationtill samtliga lärandemål, angående sin forskning för samtliga deltagare.

Compulsory elements : Gruppdiskussioner och plenumdiskussioner är obligatoriska. Vid frånvaro kan studenten iviss utsträckning kompensera detta genom att lämna in skrivna svar angående de fall som diskuterats.

Number of students : 30 35 Selection of students : Urvalet baseras på 1) datum för doktorandregistrering (där tidigare registreringsdatum

har förtur), 2) kursplanens relevans för den sökandes doktorandprojekt (enligt motivering). More information :



[email protected]



[email protected]














More information :



[email protected]



[email protected]

Title : Methods for life course epidemiology




Specific entry requirements : Knowledge equivalent to "Epidemiology I: Introduction to epidemiology","Biostatistics I: Introduction for epidemiologists", "Epidemiology II: Design of epidemiological studies","Biostatistics II: Logistic regression for epidemiologists" and "Biostatistics III: survival analysis for epidemiologists"or corresponding courses.

Purpose of the course : The course critically reviews life course theory and methods for analysis of longitudinaldata with applications to life course epidemiology. A special focus is put on discussing and applying methods formediation analysis.

Learning outcomes : After successfully completing this course, the student is expected to be able to: Discussthe most common life course models and their implications for health policy Evaluate strengths and limitations inusing register data for research in life course epidemiology Explain the applicability of visualization techniques forresearch in life course epidemiology Identify and apply appropriate methods for mediation analysis Performmediation analysis, and interpret and communicate the derived results Critically appraise evidence from lifecourse epidemiological studies.

Contents of the course : This course focuses on an overview and critical discussion of life course theory andmethods for analysis of longitudinal data with applications to life course epidemiology. We shall review, discuss andapply different approaches to addressing common challenges in registerbased, life course and intergenerationalresearch through both methodological innovations and adaptation of existing statistical methods. Examples oftechniques to be discussed and applied include methods for visualizing and modeling changes in categoricalvariables, modeling the effects of binary exposure variables over the life course, and techniques for mediationanalyses. We shall also discuss and apply concepts and methods from the field of causal inference to life coursestudies. The statistical software used in the lectures and computer labs is Stata.

Teaching and learning activities : Lectures, computer labs and individual and group work involving analysis ofreallife research problems using longitudinal data and a statistical software (Stata).

Examination : To pass the course, the student has to show that the intended learning outcomes have beenachieved. The assessment methods used in this course are individual and group assignments (formativeassessment) and an individual takehome examination (summative assessment). The focus will be on application ofmethods to research problems and interpretation of results, rather than mathematical detail. The examination isviewed as contributing to the development of knowledge, rather than a test of that knowledge. Students who donot obtain a passing grade in the first examination will be offered a second examination within two months of thefinal day of the course.

Compulsory elements : Individual written examination (summative assessment). Number of students : 8 25


More information : The individual examination will be performed as a takehome examination.

Course responsible : Anita Berglund


[email protected]


[email protected]

Nobels väg 13

17177

Stockholm

Title : Introduction to R data management, analysis and graphicalpresentation




Specific entry requirements : Basic statistical knowledge (e.g. taken "Basic course in medical statistics" orsimilar course)

Purpose of the course : To increase the doctoral student's skills in data analysis and data presentation. Learning outcomes : After attending the course, the student will be able to use R for data management,

statistical analysis and graphical data presentation. The student will be able to install new functions in R. Contents of the course : R is a powerful software/programming language for data analysis and graphical

presentation. R is freeofcharge, and in most cases a useful alternative to commercial statistical software. Theprogramming language is completely textbased, making it challenging compared to software with a graphical userinterface. However, it offers greater flexibility, better control over analyses and an automatic documentation ofperformed analyses. The course focuses on structure and basic functions of the R programming language . Aselection of functions for data management, statistical analysis and graphics is presented. The methods includedare commonly used methods in clinical medical science (e.g. ttest, ANOVA, chi2test, regression and survivalanalysis, box, line scatter, and bar plots). The course focuses mainly on how the various methods are applied in Rand not their theroretical background, underlying assumptions or the theoretical intepretation of the results.

Teaching and learning activities : Lectures and online video material, practical exercises (individual and groupassignments), peer assessment of other students' solutions.

Examination : Written examination Compulsory elements : The practical exercises and the peer assessments of these are compulsory. Students

unable to complete the exercises in time due to e.g. illness can get an extention of the deadline. Number of students : 18 20


More information : The course is held at Karolinska University Hospital Huddinge. Course dates: 4/4, 6/4, 13/4,20/4, 27/4, 4/5, 7/5. Between these course dates, there will be deadlines for mandatory home assignments. Laptoprequired for programming exercises. The duration of the course has been extended from 1.5 to 2.5 credits. Theevaluation report link refers to the previous, shorter version of the course (course number 2657).

Course responsible : Jonatan Lindh


[email protected]

Avd. för klin. farmakologi, C1:68 Karolinska universitetssjukhuset Huddinge

14186 Stockholm

Contact person :

Marine Andersson Institutionen för laboratoriemedicin

08585 81064 [email protected]

Title : Anaesthesia, analgesia and surgery (mice and rats)



Level : Doctoral level Responsible KI department : Comparative medicine

Specific entry requirements : Students need to complete a laboratory animal science course on how to carry outscientific procedures on the appropriate animal species i.e. EU Function A or equivalent course.

Purpose of the course : Training in anaesthesia, analgesia and surgery is both essential, and a legal requirement,for all those who need to undertake such procedures on laboratory animals. Applying appropriate techniques to invivo studies enhances outcomes from research studies, reduces data variability, and is perceived as ethicallyacceptable. The course includes problem solving sessions, which encourage students to reflect on the application ofthe course content in their own research area, and encourages them to discuss and explain their work with otherparticipants.

Learning outcomes : The course is designed to meet the learning outcomes specified by the trainingrecommendations supplied as an annex to EU Directive 2010/63/EU. Swedish legislation was amended to meet therequirements of this Directive in 2013. After completion of this course, the students should be able to meet thedefined learning outcomes as set out in the EU modules 20, 21 and 22. Each module requires both theoreticalknowledge, and acquisition and demonstration of practical skills. The list of suggested learning outcomes by theendorsed guidelines is comprehensive, but in summary, participants will acquire the knowledge and skills toanaesthetize animals safely and humanely, assess and alleviate postsurgical pain, and be able to conduct surgicalprocedures competently, using appropriate aseptic technique.

Contents of the course : The course provides guidance and information to individuals who, during their researchwork with animals, will need to apply sedation or anaesthesia and who will undertake surgical or other painfulprocedures. It includes details of methods of assessing, preventing and alleviating animal pain. The course willinclude training in the most recently developed behavioural measures of pain, including use of grimace scales.Monitoring of animals during anaesthesia, and coping with problems and emergencies are explained anddemonstrated. Potential interactions between anaesthetic and analgesic agents and specific research protocols arealso explained and discussed. Training is given in the principles of preoperative animal assessment and care,preparations for surgery, aseptic technique and the principles of successful surgery. The module providesinformation about possible complications, postoperative care and monitoring along with details of the healingprocess. It also covers more practical elements for example the demonstration of commonly used instruments andprovides an opportunity for trainees to practice some of the practical aspects of basic surgical technique, such asmethods of suturing, and using appropriate nonanimal models.

Teaching and learning activities : The course will adopt a blended learning approach that combines seminars,discussions, interactive sessions and practical components. Nine seminars will be given: Introduction toanaesthesia basic principles and definitions, anaesthesia and the 3Rs (replacement, reduction and refinement),selection of anaesthetics. Preparation for anaesthesia, inhalational anaesthesia. Injectable anaesthetics. Monitoring anaesthesia and intraoperative care. Long term anaesthesia and use of ventilators andneuromuscular blocking drugs. Postoperative care fluids, nutrition and nursing care. Pain assessment and painalleviation. Surgery and aseptic techniques (1). Surgery and aseptic techniques (2). Two interactive problembased sessions will be included, using Audience response systems to facilitate discussions. An audience responsesystem will also be used throughout the seminars to encourage participation and engagement by the students. Theseminars incorporate video material and supplemental material is provided via online elearning components. Laboratory practical sessions (56 hours) on anaesthesia and surgical skills are interspersed with the seminars andinteractive sessions.

Examination : Practical skills are assessed during the laboratory session using DOPS (direct observation ofpractical skills), and a short answer/multiple choice question final written examination is held following conclusionof the course. A pass/fail criteria will be used as a global rate for this course, a level of supervision for theprospective work on animals will be assigned, as suggested in the EU guidelines endorsed by the Swedishcompetent authority for the protection of animals used in science.

Compulsory elements : All sessions and active student participation are compulsory if the student is to beprovided with certification of the successful completion of the course. Missed parts of the course as a consequenceof a welljustified absence will need to be compensated after agreement with the course director e.g. with writtenassignment or in future course editions.

Number of students : 8 16 Selection of students : Selection will be based on the relevance of the course syllabus for the applicant's doctoral

project (need to use anaesthetic or surgical techniques in rodent models), which will be according to writtenmotivation. If necessary, additional selection criterium will be used based on the date for registration as a doctoralstudent (priority given to earlier registration date).

More information : Facetoface teaching will be held from Tuesday to Thursday between approx. 9am and 5pm.Location: Learning Lab, von Eulers väg 4A, 2nd floor. Key topics of this course include basic and advancedanaesthetic and analgesia, and basic surgical procedures on laboratory animals, with focus on anaesthesia, painrecognition and analgesia in rodent models. The main instructor of this course is internationallyrecognized expertProfessor Paul Flecknell, MA, VetMB, PhD, DECLAM, DLAS, DECVA, (Hon) DACLAM, (Hon) FRCVS, author of theHandbook Laboratory Animal Anaesthesia, 4th Edition, and a number of research publications and educational

material in the field.

Course responsible : Rafael Frias

Comparative medicine 085246660

[email protected]

Contact person :

Title : Translational Paediatric Oncology in the Era ofImmunotherapy and Omics




Specific entry requirements : Purpose of the course : To enable to obtain a comprehensive overview of the different domains within childhood

cancer research and to understand the historical milestones forming the paradigms that have led to a cure of 8 outof 10 children with cancer To give an insight into the current limitations and problems of childhood cancertreatment To enable to get an understanding of how new methodologies in molecular biology increase ourknowledge about tumourigenesis and tumour evolution. To provide an opportunity to hypothesise and developideas about how to cure the remaining 2 out of 10 children with cancer.

Learning outcomes : At the end of the course the students should be able to: Summarise the basicepidemiological data, tumor biology and genetics, novel therapy modalities like targeted therapies andimmunotherapy, including side effects, late effects and follow up within the field of paediatric oncology. Discussthe ethical issues around childhood cancer research. Describe and understand the principles of treatment,existing therapies, new targeted therapies and personalized medicine. Explain and theorize about the linkbetween cancer cell biology, tumour microenvironment, immunology, genetics, and drug treatments current anddevelopment of new drugs. Understand and discuss the current experimental methodology applied to pediatriconcology research such as in vivo, in vitro and in silico models. Critical comment on research findings regardingpaediatric oncology research.

Contents of the course : Introduction to research on paediatric oncology for PhD students and junior postdocs,with research projects in this specific area or in an adjacent area. The students will be presented with and willdiscuss problems, possibilities, and research models that are specific for the research area of paediatric oncology.The course will provide a general introduction to the field and focus on distinct, but interconnected topics specificfor paediatric oncology, namely ethics, epidemiology, tumor biology and genetics, existing and novel targeted drugtreatments as well as immunotherapy, and side effects, late effects and follow up. The last day will be dedicated toa symposium with invited lecturers that are internationally renowned expert in their fields.

Teaching and learning activities : Lectures, seminars, group exercises with supervised discussions. To promoteactive discussion and participation, each student will prepare a poster and a short oral presentation on their currentor intended research to be submitted no later than two weeks before the course start. The course will becomplemented with a oneday research mini symposium.

Examination : To pass the course the students must show that they have reached the learning outcomes of thecourse. Each students should prepare a scientific poster on an actual or hypothetical childhood cancer researchproject, including one of the following topics: epidemiology, register research, tumour biology and genetics, noveltherapy modalities like targeted therapies and immunotherapy, and give an oral presentation of the poster andanswer to critical questions of the audience consisting of the course leaders and course participants. Eachparticipant in the course needs to be able not only to answer questions in a satisfactory way but also to raiserelevant questions and to be able to discuss in line with the intended learning outcomes of the course.

Compulsory elements : All course activities are compulsory. Absence can be compensated for by other activitiesin agreement with the course leaders.

Number of students : 8 28 Selection of students : Priority will be given to registered doctoral students with projects concerning pediatric

oncology research who are in the later phase of their doctoral education. Thereafter student in an earlier phase willbe prioritized while acceptance of post docs will be subjected to availability.

More information : Monday to Thursday are organized as full days with lectures, seminars and discussions. Thecourse concludes with a symposium on Friday with several known experts in the field. The course will be held atCancer Centre Karolinska (CCK) and the Astrid Lindgren Children's Hospital (exact rooms will be announced in duetime). The symposium will take place at the Nobel Forum.

Course responsible : Anna Nilsson

Department of Women's and children's health

[email protected]

Contact person : Désirée Gavhed

Institutionen för kvinnors och barns hälsa

[email protected]

Nikolas Herold Institutionen för kvinnors och barns hälsa

[email protected]

Malin Wickström Institutionen för kvinnors och barns hälsa


Teresa Frisan Institutionen för cell och molekylärbiologi


Berzelius väg 35

S17177

Stockholm

Title : Microbiota, metabolism and immunity in the development andtreatment of malignancies




Specific entry requirements : Purpose of the course : The microbiota has emerged as an important arbitrator of health and disease. The impact

of the microbiota on intestinal malignancies has gained much attraction. This course intends to impart knowledgeand introduce analytical tools to critically assess current ideas and evidence underpinning the role of the microbiotain cancer development and their effects on therapeutic regimes.

Learning outcomes : At the end of the course the student is expected to: Understand various ways to studythe microbiota in health and disease To assess what tools are available to study the function of the microbiota incancer Have basic knowledge about cancer pathology, especially gastrointestinal malignancies To explore themolecular mechanisms underlying the impact of the microbiota on cancer development To understand how themicrobiota may be a determinant in influencing treatment strategies

Contents of the course : Cancer susceptibility is sometimes defined as geneenvironment interaction. A criticalcomponent of our immediate environment is the commensal microbiota, which have a major impact on metabolismand immunity, two facets of physiology that impact on cancer. This course aims to convey current ideas and anunderstanding of the tools necessary to assess the slew of reports that link the microbiota to cancer developmentand treatment. The modules/lectures will explore how high throughput studies have been applied to assess thislink, paying particular attention to the strength of the evidence and and limitations of the anaylses. Apart fromlectures on metagenomics and metabonomics, students will be introduced to basic diagnostic cancer histopathologyand molecular diagnostics, as well as to breakthroughs in exploratory translational research. A final goal is that thestudents shall be able to critically assess the research published on this subject and formulate the necessary criteriato test their assumptions. This can be in the form of a defined research project.

Teaching and learning activities : The course will be organized as a series of lectures coupled with defineddiscussion topics, led by selected lectures. All students are to participate in the scheduled group discussions withinvited experts/lecturers. Students are also very much encouraged and expected to engage in critical dialecticconstructive discussions throughout the course ("Filip och Fredrik pedagogic"). The students will be provided beforethe starting of the course with material that they should read in advance and that will be used as base for thelectures and discussions.

Examination : To pass the course the students must show that they have reached the learning outcomes of thecourse. This will be assessed formatively during the group discussions with the lecturers where students will bedivided in group of 23, and by an individual assessment based on writing a microbiotacancer project related totheir own research interests.

Compulsory elements : Attendance to the lectures, scheduled discussions and seminars is compulsory. In specialcases, with limited absence, the student can compensate with a written report upon discussion with the courseorganisers.



More information : We intend to start with a brief presentation of research interests of participants and theirexpectations of the course. 1. Three and a half days of lectures, seminars and theory discussionsessions 2. One lab visit (microbiota sequencing laboratory) 3. Two afternoons of research proposalpreparations 4. Presentation of research proposal 

Course responsible : Velmurugesan Arulampalam

Department of Microbiology, Tumor and Cell Biologi 0852486670

[email protected]

Theorellsväg 3

17177 Stockholm

Contact person :

Title : Advanced cancer biology




Specific entry requirements : Basic course in tumour biology and oncology. Purpose of the course : The course aims to provide advanced, cutting edge preclinical and clinical knowledge in

the field of cancer biology. Learning outcomes : At the end of the course the students should: Have acquired an updated overview of the

cutting edge research activities within the fields of cell and tumor biology. Be able to show analytical and criticalthinking when discussion advanced problems in cell and tumor biology, beyond what is found in text books, andevaluate the relevance of the topics presented in the context of their own research activities and PhD studies. Beable to discuss important aspects of tumor biology, including apoptosis, cell cycle, cancer stem cells, differentiation,virus and bacteriaassociated cancer, tumor immunology and effects of chronic inflammation in carcinogenesis,cancer genetics and epigenetics, transcriptomics, proteomics and metabolomics of cancer, tumormicroenvironment, angiogenesis, metastasis, tumor heterogeneity and development of new treatments as well askey issues in clinical cancer research.

Contents of the course : The lecturers will give a comprehensive and pedagogical overview of the research areaas well as an indepth discussion of their own research, related, but not limited, to the following topics: apoptosis,cell cycle, cancer stem cells, differentiation, virus and bacteriaassociated cancer, tumor immunology and effects ofchronic inflammation in carcinogenesis, cancer genetics and epigenetics, transcriptomics, proteomics andmetabolomics of cancer, tumor microenvironment, angiogenesis, metastasis, tumor heterogeneity and developmentof new treatments as well as key issues in clinical cancer research.

Teaching and learning activities : The course will consist of about 20 lectures, with approximately 45 minutesper lecture, at least once a week during one semester. Each lecture will be followed by an open discussion betweenthe students and the invited speaker led by one of the course organizers: this format will provide time forhighlighting key issues within the specific topic and will enhance the possibility for the students to expand theirnetworking activities due to direct contact with experts in the field. To increase the learning process and tostimulate the reflection on the course topic, the students will be required to study the most recent literature, stillnot present in the text books within the presented fields, prior to each seminar. Throughout the course period, thecourse organisers will have regular meetings with the students to follow up the learning process of each individualparticipant as well as to receive feedback from the students.

Examination : The students have to show that the intended learning outcomes of the course are reached. This willbe individually assessed during the participation in the informal discussions after the seminars and on the basis anindividual written assessment, in form of a project description where one or more topics presented during thecourse should be integrated within the student own research project (Max one and half A4 page, stating: theobjective of the project, a brief description of the research plan, and the significance). The project descriptionshould be handed in maximum three weeks after the completion of the course to the organizers.

Compulsory elements : Attending the lectures and the written essay are compulsory. Missed seminars can becompensated by other activities after discussion with the course leader.



More information : The course is organized to contain approximately 20 lectures of 45 min plus 15 mindiscussion, held once per week during the semester by invited national and international prominent researchers. Alllectures are held in the MTCseminar room, A 302, Nobels väg 16, KI Campus Tuesdays at 1 pm, unless elsestated.

Course responsible : Larsgunnar Larsson


lars[email protected]

Contact person : Galina Selivanova Institutionen för mikrobiologi, tumör och cellbiologi

[email protected]

Jonas Fuxe Institutionen för medicinsk biokemi och biofysik

Title : Advanced Cell Culture modelling with human inducedpluripotent stem (iPS) cells



Level : Doctoral level Responsible KI department : Department of Neuroscience

Specific entry requirements : Purpose of the course : The purpose of the course is to give students training on advanced cell culturing and how

to implement them in medical research for cancer treatment and regenerative medicine. The participants will begiven the opportunity to develop basic handson skills in how to culture human iPS cells and other human cell types

Learning outcomes : After the course, the student is expected to: Be able to describe the basic knowledge onhow to culture human induced pluripotent stem (iPS) cells. Be able to critically assess how cultured cells can beused in therapies today. Understand organoid culturing and their role in medical research. Acquire basicknowledge on tissue engineering and critically assess their future implementation in research. Discuss how cellcultures can be developed in medical research and how to implement their use within the frame of their current andfuture research activities.

Contents of the course : The course covers a wide variety of topics involving cell culturing, including; sources(human) of cells for culturing, growth conditions, monitoring, basic quality analysis of cells in culture, culturing ofcells in monolayers, as organoids and in cocultures with other cells types. Strong emphasis will be given topractical handson sessions. Throughout the course, the concept of good manufacturing practice (GMP) for humancell cultures and the practical use of cell cultures for disease modeling, regenerative medicine and cancer treatmentwill be strongly implemented.

Teaching and learning activities : To provide a comprehensive and practical hands course, several teachingactivities will be combined during the course, including lectures, laboratory practice, group discussion, presentationof a research proposal and study visit to laboratory implementing human cell cultures in production.

Examination : The course assignment will consist on a formative assessment based on individual presentation of aresearch proposal. The proposal is focusing on the study design of the cell culture experiments demonstrating thatthey can design a cell culture experiment and put cell culturing into context of a specific scientific question, relatedto their scientific activities. The course organizers will lead the examination, providing feedback during thepresentation in line with the concept of formative assessment, and they will be further responsible for thesummative individual assessment.

Compulsory elements : Laboratory practice, group tasks and presentations are mandatory Number of students : 8 16

Selection of students : Selection will be based on 1) the relevance of the course syllabus for the applicant¿sdoctoral project (according to written motivation), 2) date for registration as a doctoral student (priority given toearlier registration date)

More information : Lectures will be held at the department of Neuroscience in Solna. Handson cell culturing willbe performed at the MTC course lab in Solna.

Course responsible : Anna Falk

Department of Neuroscience

[email protected]

Contact person : Malin Kele

Institutionen för neurovetenskap

[email protected]

Title : Cell cycle, cancer and anticancer targets



Level : Doctoral level Responsible KI department : Department of Cell and Molecular Biology

Specific entry requirements : Purpose of the course : The course aims to provide the students with an updated overview of the cutting edge

research activities within the fields of cell cycle and oncology focusing on the role of cell cycle (de)regulation as acause and possible treatment opportunity for cancer.

Learning outcomes : The course is organized to encourage analytical and critical thinking. At the end of thiscourse, students should: be able to understand, analyze and criticize current strategies towards exploiting theavailable information on cell cycle regulation, tumor suppressors and oncogenes for the development of noveltherapeutics, evaluate the relevance of the topics presented for their future research activities and PhD studies

Contents of the course : The course contains approximately 10 seminars/lectures, held by invited national andinternational prominent scientists, as well as 15 hours of discussion/problembased learning. The speakers will beasked to give a comprehensive and pedagogical overview of the research area as well as an in depth discussion ontheir own research. Each seminar will be followed by a discussion led by the course organizers where the studentsare encouraged to interact with the invited speaker. To enable a fruitful discussion the students will have to readrelevant literature in the field in advance of each seminar. The topics presented will cover the main aspects of thefollowing themes: 1. Cell Cycle molecular overview and biological functions 2. Oncogenes and tumor suppressorswithin the cell cycle 3. The connection between cell cycle and the hallmarks of cancer 4. Targeting aberrant cellcycle signaling in cancer current therapeutics 5. Technological advances in cancer cell cycle therapeutics Eachday will be dedicated to a cellcycle phase/process and these themes will be incorporated.

Teaching and learning activities : The course is fulltime. It will consist of approximately of 3 hourslectures/day. Each lecture will be followed by a discussion led by one of the course organizers. To increase thelearning process and to stimulate the reflection on the seminars, the students will be required to study the mostrecent literature, still not present in the text books within the presented fields in advance of each seminar. Further,students will be required to individually present and discuss specific aspects of the content.

Examination : As assessment, students will be evaluated based on their contributions i) to the discussion duringthe problembased learning of each topic; ii) in connection to an individual presentation on a specific topic assignedat the beginning of the course.

Compulsory elements : Students are expected to attend and participate in all lectures, presentations anddiscussions. In the case of absence, the student will be asked to read a relevant review and/or original researcharticle on the topic missed, summarize it and discuss it with the organizer of the course at a convenient time byappointment.



More information : Information about the venue and material necessary for the course will be communicated tothe students in due time.

Course responsible : Arne Lindqvist

Department of Cell and Molecular Biology

[email protected]

Contact person : Per Hydbring

Institutionen för onkologipatologi

[email protected]

Title : Bioinformatics analysis of gene regulation in omics data andits applications to medical problems




Specific entry requirements : Purpose of the course : To increase the understanding of the basic principles of bioinformatics and to gain

practical skills in bioinformatics analysis of genomic sequencing data. Learning outcomes : After the completed course, the participants will be able to understand the principles and

perform basic bioinformatics analysis of genomics sequencing data. The participants will be able to planexperimental designs and to critically evaluate the appropriateness of the different sequencing based omicsmethods and technologies for genomewide gene regulation studies.

Contents of the course : Principles of gene regulation in nondisease cases and dysregulation in diseases atindividual locus level as well as on genomewide level. Principles of sequencing based genomics technologies andcorresponding bioinformatics data analysis. Concrete bioinformatics data analysis by the students of selectedpublished projects.

Teaching and learning activities : The course consists of preparatory work, lectures, discussion, seminars andhandson bioinformatics analysis.

Examination : The students will be examined for all learning outcomes by their performance in (a) submittedreplies to tasks given for course week 1, (b) discussions and quizzes during the course week 2, and (c) individualpresentations at the last course day of their bioinformatics analysis results conducted during course week 2.

Compulsory elements : The preparation is done in the first course week without the need to be present onsite.Week 2 consists of tasks, lectures, discussions, seminars and handson practicals. Both parts are compulsory.Absence has to be compensated for according to the instructions from the course leader.



More information : The course is given in collaboration with the RIKEN Division of Genomic Technologies(http://www.riken.jp/en/research/labs/clst/genom_tech/). The course faculty consists of invited speakers from theRIKEN Division of Genomic Technologies and Karolinska Institutet. Note that during the first week of the course theparticipants will work on their own at their own departments and there is no room/study space booked for this part.The second week of the course takes place at CMB, KI, seminar room A216, entrance Berzelius v 35.

Course responsible : Carsten Daub

Department of Biosciences and Nutrition

[email protected]

Contact person : Matti Nikkola

Institutionen för cell och molekylärbiologi

[email protected]

Title : Grundkurs i SPSS



Level : Forskarnivå Responsible KI department : Department of Clinical Sciences, Danderyd Hospital

Specific entry requirements : Purpose of the course : Kursen kommer att ge dig solida grundkunskaper i statistikprogrammet SPSS, du lär dig

bl a hur man lägger upp och strukturerar ett dataset, och hur man kan importera material från andra applikationertill statistikprogrammet SPSS och att tvätta data så att dessa blir i analyserbart skick. En av de viktigaste delarnai analysen är att beskriva det datamaterial som har samlats in. Vi går grundligt igenom olika procedurer för att"lära känna" olika typer av variabler. Detta inkluderar även omkodning av variabler, skapa nya variabler frånbefintliga och selektera ut individer som uppfyller vissa givna villkor.

Learning outcomes : Efter kursen skall doktoranden: Ha grundläggande kunskaper om statistikprogrammetSPSS för att skapa strukturerade datafiler, modifiera data, samt skapa grafer och tabeller med hjälp avprogrammets menysystem. Självständigt kunna skapa en datafil utifrån ett protokoll/enkät och mata in data. Självständigt kunna definiera, sortera, modifiera och selektera data för enklare situationer. Självständigt kunnaskapa grafer och avancerade tabeller och göra enklare redigeringar. Ha en grundläggande insikt om olika typerav fel som kan uppstå vid datahantering.

Contents of the course : Olika procedurer för att lära känna olika typer av variabler. Detta inkluderar ävenomkodning av variabler, skapa nya variabler från befintliga och selektera ut individer som uppfyller vissa givnavillkor. Den beskrivande analysen omfattar både produktion av olika tabeller såväl som val av diagram. Du lär digvilka typer av tabeller och diagram som är lämpliga beroende på de variabler du studerar. För att erhålla såpresentationsfärdiga rapporter som möjligt lär vi oss även att redigera resultatet av analysen. Ändamålet är atthjälpa dig att effektivisera ditt arbete och snabbt komma igång med SPSS.

Teaching and learning activities : Denna kurs som sträcker sig över 5 dagar (2 dagar workshop + enövningsuppgift med avslutande seminarium).

Examination : Examination av kursen består av en hemuppgift som redovisas muntligt och skriftligt. Compulsory elements :


motivering), 2) datum för doktorandregistrering (där tidigare registreringsdatum har förtur). More information : Måndag och tisdag hålls kursen fysiskt vid Danderyds sjukhus hus 18 plan 5. Lokal

annonseras senare.

Course responsible : Fredrik Johansson

Department of Clinical Sciences, Danderyd Hospital

[email protected]

Contact person :

Title : Observation and visual methods in health care sciencesresearch




Specific entry requirements : Purpose of the course : To develop knowledge about the methodological underpinnings of visual and observation

methods, which are utilized within health care sciences research Learning outcomes : Based on theoretically relevant tools, upon completion of the course the student is expected

to be able to: analyse and explain the rationale for methodological approaches using participant observation,photographic data generation, and video observations. critically compare different visual methodologicalapproaches in relation to research questions. demonstrate practical skills with theoretically grounded argumentsfor the choices made in data gathering and analysis related to different visual methods. demonstrate criticalreasoning about ethical issues concerning the collection of, and working with, visual data in healthcare sciences.

Contents of the course : Engaging the visual senses in healthcare science research can be done in many ways.Visual methods are here used to include ethnographic observations as well as photographic and video observations.The visual evokes elements of human consciousness that can serve as a compliment to words, when words areinsufficient or at times not at all accessible. The course content includes studies of theoretical underpinnings ofmethodological and ethical issues related to visual methods. Students will work with participant observation,photography, and video as methods while exploring these techniques in different methodological paradigms.Students will also explore different analysis with data in the course or from their own research projects.

Teaching and learning activities : This course is designed to have short trigger lectures alternated with activeexperiential learning tasks, workshops, seminars, and individual assignments/project work. The course requiresactive involvement of the student through participation in the various types of learning activities.

Examination : The examination will consist of an individual oral presentation followed by a questions and answerssession and an individual short written report. Results will be assessed as Pass/not pass.

Compulsory elements : All learning activities except the lectures are mandatory. Absence can only becompensated for in agreement with the course organizer.



More information : Course dates are set for: 57 March, 1113 April, and 2325 April, 2018. The course will havecampus attendance at Alfred Nobels Alle 23 (Flemingsberg) and online.

Course responsible : Eric Asaba


[email protected]

Contact person :

Title : Human Papilloma Virus from molecular biology to globalhealth an eLearning course




Specific entry requirements : The precourse knowledge prerequisites are BSc or equivalent in biomedicine. Purpose of the course : The course aims to provide knowledge of the scientific background of the biology

of Human Papilloma Virus (HPV) infection, the burden of HPV associated diseases, screening and vaccination. Inthis oneweek course on the global health importance of Human Papilloma Virus (HPV) infection, you will learnabout HPV molecular biology and mechanisms of virusinduced cancer, screening of cervical samples, using HPVtesting as well as bioinformatic analysis and methods for quality assurance and followup of programs of HPVbasedscreening and vaccination. You will explore how this knowledge can be applied to reduce the risk of disease. Takingpart in an online discussion thread will give you a chance to reflect on the impact of HPV vaccination and screeningin society. You will also learn about HPV analysis methods.

Learning outcomes : On completion of the course the student should be able to: 1 Understand and describe HPVinfection and the burden of HPVassociated diseases. 2 Understand and describe methods for detection of HPV andthe bioinformatics methods for HPV classification. 3 Describe the best practice for organized cervical screening. 4Assess internationally standardized quality indicators of cervical screening 5 Interpret and validate results fromscreening and vaccination and their implications on the cancer burden.

Contents of the course : Block 1, Day 13: Molecular Biology of HPV Block 2, Day 34: Cervical Screening andHPV vaccination Block 3, Day 56: Quality Assurance and Followup of HPVtargeted Cancer Control

Teaching and learning activities : The course is internetbased and is open for 5 weeks in total. Each day in thefirst week video lectures, assignments relating to the contents of the video lectures and supplementary material inthe form of open access scientific articles will be released. In some cases, the assignments will be in the form oflecture quizzes and in some cases you will be asked to post in a discussion forum.

Examination : You will need to have completed the learning activities before being able to participate inthe final examination. Examination will be scheduled on two occasions, one immediately after the first two weeksand the other after five weeks. Using a webcam, you will identify yourself by taking a photo of yourself togetherwith your governmentissued photo ID. Examination will be internetbased in the form of multiple choicequestions and writing assignments.

Compulsory elements : Participation in lecture quizzes, discussion thread, and examination is mandatory. Thediscussion thread will be organized and supervised according to the established format of the open sourceeLearning software Moodle. The teachers supervising the discussion thread will ensure that the participants reachthe predefined educational goals.



More information : This is an online course.

Course responsible : Joakim Dillner


[email protected]

Forskningsgatan F46 Huddinge Sjukhus

14148 Stockholm

Contact person :

Ulla Rudsander Institutionen för laboratoriemedicin

[email protected]

Title : Introduction to teaching




Specific entry requirements : Purpose of the course : The purpose of this course is to introduce a variety of teaching and learning methods,

and to stimulate a reflective approach to teaching in order to enhance students' meaningful learning and activeinvolvement.

Learning outcomes : At the end of the course we expect you to: Be able to explain general aspects of how tofacilitate student learning in different teaching situations Be able to reflect upon own teaching experiences anduse educational concepts in a discussion about teaching and learning

Contents of the course : During the course we will discuss and elaborate on practical issues regarding teachingand learning in laboratory, seminars and lectures. We will discuss and work with ways to challenge students andwhat to do to facilitate their learning. Course participants will observe (auscultate) teaching and reflect upon theirexperiences. We will touch upon the role of the teacher and KI teaching policies as well as strategies for coping withstress.

Teaching and learning activities : The course is designed to promote active learning and a variety of teachingand learning strategies will be used during the course. Examples are lectures, small group discussion, peerteaching, group work, literature studies, auscultation of teaching and reflection in groups.

Examination : To satisfactorily complete this course you must demonstrate that you have reached the learningoutcomes by orally presenting your reflections of literature studies and auscultation of teaching.

Compulsory elements : The assessment seminar the last day of the course is mandatory. If absent, the studentneed to present his/her knowledge at a separate occasion.

Number of students : 15 30 Selection of students : Priority will be given to doctoral students who have just started or soon will be involved in

teaching and that have no teacher training. More information : The course is based on theories of experiential learning, a reflective approach and learning

through active participation and collaboration. In order to learn as much as possible from the course it is importantto be present at scheduled meetings and, where appropriate, be prepared for them. The course is scheduled 13March, 22 March and 12 April. In addition, time for reading and auscultation must be planned by the courseparticipants. The course is given in English. The course is equal with the previous course number 2686 Introduction to teaching at KI.

Course responsible : Mohammed Seed Ahmed Department of Learning, Informatics, Management and Ethics

Mohammed.Seed[email protected]

Contact person :

Margareta KrookBrandt Institutionen för lärande, informatik, management och etik


Title : Mixed methods: integration of qualitative and quantitativedata within applied health research




Specific entry requirements : Students must be familiar with the basics of qualitative and quantitative researchbefore joining the course.

Purpose of the course : Health research problems are complex phenomena with multiple dimensions which aredifficult to assess using quantitative or qualitative methodologies alone. Mixedmethods research is a methodologythat combines both qualitative and quantitative research allowing the researcher a more comprehensiveunderstanding of the issue under study. Mixedmethods pragmatic research designs provide strengths that offsetthe weakness of both quantitative and qualitative studies. This course will provide Ph.D students with thetheoretical tools and practical experience to design, conduct and report mixedmethods studies in health research. Learning outcomes : At the end of the course the students will: 1. Design a mixedmethods research question(s). 3. Apply different mixedmethods research designs to a health problem. 4. Write a mixedmethods researchprotocol. 5. Report the results of a mixedmethod study. 6. Use mixedmethods to design and evaluateinterventions studies. 7. Evaluate the quality of scientific manuscripts using mixedmethods designs.

Contents of the course : 1. Definitions of mixedmethods research. 2. Worldviews and mixedmethods research. 3. Writing a mixedmethods research protocol. 4. Choosing a mixedmethods design. 5. Integrating results inmixedmethod studies. 6. Reporting and disseminating mixedmethod studies. 7. Application of mixedmethodsresearch in interventions studies. 8. Evaluating the quality of mixedmethods studies.

Teaching and learning activities : The course will start by discussing the quantitative and qualitative researchdesigns and how both research paradigms can be combined to strengthen each other. The course will combinefacetoface lectures, online practical assignments/discussions, selfstudy and oral presentations. Facetofacelectures and other activities will be conducted once a week for a period of five weeks. Once a week lectures willallow the students to reflect on the given material and to apply this new knowledge to the practical assignments.Practical assignments will be discussed with the group and feedback will be given.

Examination : Course assignments and take home examination. Both will be graded as fail or pass. In order topass the course, the student need to pass the assignments and the take home examination. The courseassignments will guide the students through the steps needed to design a mixedmethods protocol. Take homeexamination. The aim of the examination is to test the students on what they have learned over the duration of thecourse and how well they can apply it. The take home examination will consist on open ended questions where thestudents will appraise the quality of published mixedmethods studies and the structure of mixedmethodsprotocols among other topics. The take home exam will have to be submitted through the KI online learningplatform one week after the end of the course.

Compulsory elements : Participation in the online practical assignments and discussion will be mandatory. Number of students : 8 15

Selection of students : Eligible doctoral students, with required prerequisite knowledge, will be selected based on1) the relevance of the course syllabus for the applicant's doctoral project (according to written motivation), 2) datefor registration as a doctoral student (priority given to earlier registration date).

More information :

Course responsible : Mariano Salazar


[email protected]

Contact person :

Title : Imaging in neuroscience: with a focus on MEG and EEGmethods




Specific entry requirements : Background in medicine, biomedicine, biology, psychology, cognitive science,medical imaging, computational biology or similar.

Purpose of the course : The main purpose of the course is to provide the students with a solid understanding ofthe tools available to analyze brain activity data measured with magnetoencephalography (MEG) andelectroencephalography (EEG). The students will develop the ability to critically review results provided by differentmethods, to select the most adequate tools and experimental designs to answer different questions and to comparetheir relative advantages.

Learning outcomes : After attending the course the student should be able to: 1) follow the usual preprocessingsteps of MEG and EEG; 2) give an overview of different methods to analyze the data and explain when to use them;3) conduct MEG and EEG analysis using several methods; 4) describe different aspects of experimental design tohave in consideration when creating a MEG and EEG study; 5) give a brief overview of the usage of MEG and EEGto study brain function; 6) give a brief overview of other techniques to study brain function noninvasively anddescribe their relative merits and challenges.

Contents of the course : The course focuses on experimental design and analysis of MEG and EEG data. We willbriefly introduce the basis of the MEG and EEG signal at a neural level, and how it is measured by the differentsensor technologies applied in MEG and EEG. The data processing steps, before statistical analysis, will beexplained. The application of general linear model analysis, parametric and nonparametric tests of MEG and EEGdata will be explained, including correction for multiple comparisons. We will review experimental designconsiderations for developing MEG and EEG paradigms. The study of functional connectivity using MEG and EEGdata will be introduced. Finally, we will also introduce machine learning techniques for functional data.

Teaching and learning activities : The students will attend lectures, implement different steps of the datapreprocessing and analysis during the handson sessions, present and discuss results.

Examination : The learning outcomes will be assessed throughout the course during the handson sessions wherethe students have to perform data analyses. The students will also complete a more extensive assignment based onone of the handson sessions. In the final day of the course the students will present and discuss their assignmentswith the rest of the group.

Compulsory elements : All parts of the course are mandatory. Absence can be compensated for by completion ofan assignment on the material covered in the missed course instance.



More information :

Course responsible : Daniel Lundqvist


[email protected]

Contact person :

Title : Mouse necropsy



Level : Doctoral level Responsible KI department : Comparative medicine

Specific entry requirements : Students need to have completed a laboratory animal science course on how tocarry out scientific procedures on mice i.e. EU Function A or equivalent course.

Purpose of the course : This twoday course will provide the students with the theoretical background ofperforming mouse necropsies, including procedures and methods to preserve organs and tissues for furthermorphological analysis. The course will primarily be practical. This should ultimately enable the students to performcomplete mouse necropsies in a standardized and reproducible way.

Learning outcomes : After completion of this course, the participants of the course should 1) know how to carryout a necropsy in a mouse according to good veterinary and scientific practice, 2) understand the requirementsneeded to perform organ sampling through a standardized necropsy protocol. The practical learning outcomesbased on a supervised training of mouse necropsies will provide the students with a basic knowledge to describeorgan changes, how to document these and preserve the organs in such a way that further analysis can beperformed on tissues that show a minimum of autolysis, thus providing optimal conditions for extracting usefulinformation from mice.

Contents of the course : This course will provide a basic foundation to individuals who, perform research usingexperimental mouse models, and have to conduct a postmortem examination to analyze morphological changeseither due to experimental manipulation or due to introduced genetic changes. The course will provide a theoreticalbackground to standardized mouse necropsies, sampling of organs, alternative ways of preserving these for furthermorphological analyses, as well as trimming of the organs and preparing these for sectioning for later evaluationusing microscopy. A basic description of terms used to describe gross changes will be provided both in lectures andthrough recommended literature. The main part of the course will be devoted to practical necropsy training, wherethe participants will be actively supervised during the training.

Teaching and learning activities : The course will be based on prereading material on basic mouse anatomyand necropsy techniques, lectures on mouse necropsy, sample collection, tissue handling and fixation, practicaldemonstrations and individual practical training on such issues. Since the ultimate aim is to provide courseparticipants with enough practical training to enable them to perform independent necropsies and tissue samplingthis two day course will be split into 1+1 days with an intermittent period for personal training and reflection. Inthis way, participants will be given an intensive instruction and training during the first day, with a follow upproviding feedback on an individual basis and more supervised training during the second day, which will followafter one week.

Examination : Practical assessments will be carried out by direct observation of skills and documentation ofactions taken by learners during their training laboratory session. A short multiple choice question final writtenexamination will also be held at the end of the course. A pass/fail criteria will be used as a global rate for thiscourse.

Compulsory elements : All mouse necropsy sessions and active student participation are compulsory. Missedparts of the course as a consequence of a welljustified absence will need to be compensated after agreement withthe course director e.g. with written assignment or in future course editions.

Number of students : 8 10 Selection of students : Selection will be based on the relevance of the course syllabus for the applicant's doctoral

project (i.e. use of mouse models), which will be according to written motivation. If necessary, additional selectioncriterium will be used based on the date for registration as a doctoral student (priority given to earlier registrationdate).

More information : Facetoface teaching will be held on April 11 and 18, 2018 between approx. 9am and 5pm.Location: Learning Lab, von Eulers väg 4A, 2nd floor. The main instructor of this course is Dr. Björn Rozell, DDS,PhD, DVM, Professor. This course is also recognized by the LAS E&T unit, Comparative Medicine, as a ContinuedProfessional Development (CPD) activity in Laboratory Animal Science (LAS) for those working with mice as anexperimental model.

Course responsible : Rafael Frias

Comparative medicine 085246660

[email protected]

Contact person :

Title : Exploring entrepreneurial opportunities in research




Specific entry requirements : Purpose of the course : This course lays the foundation for the awareness of the potential of innovation and

entrepreneurship. It will enhance your career opportunities inside and outside academia. The course will facilitatethe discovery and identification of intellectual assets in the daily work. You will increase the awareness of thepotential of innovation and entrepreneurship, by identifying opportunities for entrepreneurship in connection toresearch. In order to develop a business idea, whether in an economic or social context, you need to apply anumber of business concepts. Relevant business tools will be introduced in order to develop a business ideastemming from research. The final step when exploring opportunities of entrepreneurship is to communicate andtest your business idea on the market. For that purpose you will learn how to package an already developedbusiness idea for introduction into the startup world.

Learning outcomes : After the course, a doctoral student shall be able to; demonstrate an understanding ofthe opportunities of innovation and entrepreneurship for utilisation of research, discover and identify intellectualassets in their own research project, explore the potential of different intellectual assets, communicate a valueproposition describing the need, approach, benefit and competition for identified intellectual assets, assess theirnew skills and reflect on possible future effects, from ones individual perspective. use design tools to gain anunderstanding for the user experience to develop solutions to user needs, transform ideas into prototypes ofproducts, services or processes, use business tools such as business modelling to develop a potential businessidea stemming from research, assess their new skills and reflect on the possible future effects, from anorganisational perspective. identify and test the potential of a developed business idea, whether in an economic orsocial context, package a business idea into a complete business plan, communicate ("pitch") the business planto people within the startup world, such as potential investors, assess their new skills and reflect on the possiblefuture effects, from a societal perspective.

Contents of the course : Exploring entrepreneurial opportunities in research is a course divided into threemodules. The first module begins with an introduction to entrepreneurship, what it is and how it can be used in thedoctoral education. The doctoral students are then given a number of practical tools to identify intellectual assetswithin daily work to use in a minor innovation projects based on their own research. The second module beginswith an introduction to prototyping using the design thinking approach. The doctoral students are then given anumber of business tools to develop a business opportunity, stemming from their research, into a business model.The last module begins with an introduction to product road map followed by a comprehensive business plan. Thedoctoral students are then given a number of practical business tools to write and test a complete business plan ofthe developed idea.

Teaching and learning activities : Each of the three modules includes three mandatory days on KI Campus andtwo days for own work. The course days are usually Monday, Wednesday and Friday. The modules are separatedwith 2 week intervals. This course lays the foundation for development of an already identified business idea. Itbegins with an introduction to prototyping using the design thinking approach. The doctoral students are then givena number of business tools to develop a business opportunity, stemming from their research, into a businessmodel. With the individual assignments the doctoral students are given the opportunity to take a closer look at theactual benefits of the new knowledge and put it into a larger context, with value for their own research and society.Learning activities consist of seminars and workshops as well as group and individual work.

Examination : The doctoral student is examined individually, on a written report, the design of a poster, thedevelopment of a prototype, business model and completion of a business plan.

Compulsory elements : Attendance is mandatory for all participants. The course director assesses if and in thatcase how absence can be compensated.



More information : Course days are Mondays, Wednesdays and Fridays, 9 in total.

Course responsible : Samer Yammine


[email protected]

Contact person :

Title : Basic Immunology




Specific entry requirements : Purpose of the course : The student will learn basic concepts in Immunology and meet the Immunology faculty

at Karolinska Institutet. This course is a good starting point for more advanced courses in Immunology. Learning outcomes : To understand basic principles of innate and adaptive immunity and how different

components of the immune system cooperate. To be able to relate, compare and understand experimental aspectsof immunerelated disease in a clinical perspective. To adapt knowledge gained of the function of the immunesystem by being able to analyze and discuss an immunological/clinical case (group project). To present the groupproject and discuss the results as well as work in pairs with clinical cases.

Contents of the course : The course is separated into two parts. In part 1 we discuss basic immunologicalmechanisms within the innate and adaptive immune response. In part 2 we apply the knowledge in clinical settingssuch as defence against infection, autoimmune and allergic disease or transplantation. Part 1: Introduction Anoverview of the immune system T cells B cells Antigenpresenting cells Innate vs adaptive immune responses Methods to study immune reactions. Part 2: Immune defence against bacterial and viral infections Primaryimmunodeficiencies Autoimmune disease Allergy Vaccination Clinical Immunology Transplantation TumourImmunology Questions and discussions Presentation of projects.

Teaching and learning activities : The course is given fulltime during a total of six days separated into twoparts. The teaching is mainly in lecture/seminar form but also includes project work studying cases individually andpairwise, as well as in small groups. The group projects are then presented orally on the last day of the course. Theproject work requires studies between the two course parts, including meetings with mentors. Course literature(Abbas) and cases are handed out at the course start. An immunological quiz is connected to the different chaptersin the book so that the student will be able to digest the relatively big material. The course is designed so thatclinically active doctors will be better able to combine it with work in the clinic (Mondays and Fridays contain noscheduled course work) .The purpose of dividing the course into two parts is that the participants should have timeto thoroughly study the literature from part 1 (fundamental immunological mechanisms) before teaching of theapplied immunology in part 2 starts. Considering the substantial literature requirement plus the cases and projectwork, we estimate that an extra 32h of study is needed, which is not included in the schedule.

Examination : Webbased exam on the course content. Oral presentations of smallgroup project work. At thisoccasion special attention is given to that all students are actively participating. The clinical cases are examined bywritten reports.

Compulsory elements : Project work and attendance at the project presentation is compulsory as well as workwith two clinical cases. In the case of absence a separate occasion is organized with presentation for the courseorganizers. The webbased exam is mandatory.



More information : The course is divided into two sessions with 3 days of lectures each, January 1618 and March68 (Tuesday to Thursday). In between these days of lectures the students work on both a group project and anindividual written assignment, including meetings with mentors and literature studies. Teachers include specialistsin different fields of immunology including both basic and clinical researchers. We will use the Abbas "BasicImmunology" as the main course textbook, but literature also includes review papers, handouts etc. The texbookthe book is free and is handed out at the course start. The course location is at the Department of MicrobiologyTumor and Cell biology (MTC), Karolinska Institutet, Solna

Course responsible : Lisa Westerberg


[email protected]

Contact person : Lisa Westerberg


[email protected]

Mikael Karlsson Institutionen för mikrobiologi, tumör och cellbiologi

[email protected]

Title : Aging Societies: Challenges and Opportunities




Specific entry requirements : Purpose of the course : This course approaches the challenges and opportunities of an aging population from a

public health perspective. It focuses on the lifelong heterogeneous aging process, and health and welfare in oldage. The course is relevant for PhD students in public health and health sciences, or students from other disciplinesinterested in aging research.

Learning outcomes : After completing this course students are expected to be able to: 1. Identify and discusssocietal challenges and opportunities that arise from an aging population, and how they can be addressed. 2.Reflect on how these challenges and opportunities can be related to her/his research. 3. Reflect on key conceptsand theories from the course, and apply them on her/his research.

Contents of the course : Life expectancy continues to increase around the world. Aging societies present societaland economic challenges, but older people are also a resource for society. The course addresses these topics andprovides knowledge on key concepts and theories in the multidisciplinary field of aging research. Attention will begiven to: The demographic shift toward an aging society: what are the challenges and opportunities for publichealth? Health trends and the interplay between morbidity and mortality in later life (e.g., compression andexpansion of morbidity) The third and fourth age The heterogeneous aging process Active, healthy, andsuccessful aging How health and health inequalities in old age are shaped by experiences and behaviorsthroughout the life course Aging within health and social care systems what are the future challenges?

Teaching and learning activities : Different strategies for teaching and learning will be used, such as lectures,seminars based on selected readings, group discussions, as well as peer reviewing. The doctoral students´proactive participation will be required.

Examination : To pass the course the student has to achieve the learning outcomes. This will be assessed throughparticipation in mandatory seminars, an individual written assignment reflecting on the course content in relation toher/his own research and also written and oral reflection on a peers individual assignment.

Compulsory elements : Active participation in group work and seminars is mandatory. If a participant is absentbecause of unforeseen circumstances, the course directors assess if, and in that case how, absence can becompensated.

Number of students : 8 25 Selection of students : Eligible doctoral students will be selected based on 1) date for registration as doctoral

student (priority given to earlier registration date), and 2) the relevance of the syllabus for the applicant's doctoralproject. To be considered, include a short description of current research.

More information : The course is extended over three weeks in order to promote reflection and reinforce learning.Lectures and seminars will be given the following dates: April 9, 11, 13, 16, 18, 20, 23, 26. The written assignmentis to be handed in on April 27. The course will be held at the Aging Research Center (ARC), Gävlegatan 16.

Course responsible : Carin Lennartsson


[email protected]

Contact person : Charlotta Nilsen

Institutionen för neurobiologi, vårdvetenskap och samhälle

[email protected]

Title : Epidemiology I: Introduction to epidemiology




Specific entry requirements : Purpose of the course : The aim of the course is to give an introduction to epidemiological theory and practice.

Learning outcomes : After successfully completing this course students are expected to be able to: giveexamples of the contribution of epidemiology to science and discuss the importance of epidemiology as a researchdiscipline. estimate and in a general way interpret measures of disease occurrence and measures of association,and describe how a specific measure is governed by the study design. explain strengths and weaknesses ofcommon epidemiological study designs. identify and explain possible sources of bias in epidemiological studies. describe theoretical models for causation and discuss the principles of causal mechanisms. apply knowledge ofepidemiological concepts when critically reviewing scientific literature.

Contents of the course : The course gives an introduction to epidemiological theory and practice. It comprisesbasic principles regarding design, interpretation, and analysis of epidemiological studies. It introduces the conceptof causation, concepts related to measures of disease occurrence and measures of association, common designs forepidemiological studies (with main focus on cohort studies), and the role of bias.

Teaching and learning activities : The course focuses on active learning, i.e. putting knowledge into practice andcritically reflecting upon the knowledge, rather than memorising facts. Different strategies for teaching and learningwill be used, such as lectures, group discussions and various forms of group exercises on selected topics.

Examination : To pass the course, the student has to show that the learning outcomes have been achieved.Assessments methods used are group assignments (formative assessments) along with an individual examination(summative assessment). The examination is viewed as contributing to the development of knowledge, rather thanas a test of knowledge. Students who do not obtain a passing grade in the first examination will be offered asecond chance to resubmit the examination within two months of the final day of the course. Students who do notobtain a passing grade at the first two examinations will be given top priority for admission the next time thecourse is offered.


Selection of students : Eligible doctoral students will be prioritized according to 1) the relevance of the coursesyllabus for the applicant's doctoral project (according to written motivation), 2) date for registration as a doctoralstudent (priority given to earlier registration date). To be considered, submit a completed application form. Give allinformation requested, including a short description of current research training and motivation for attending, aswell as an account of previous courses taken.

More information : Course dates are March 7, 9, 12, 14 and 16. The course is extended over 2 weeks (but stillfive full course days) in order to promote reflection and reinforce learning. The individual examination (summativeassessment) will be performed the last day of the course.

Course responsible : Fang Fang


[email protected]



Title : Biostatistics I: Introduction for epidemiologists




Specific entry requirements : Purpose of the course : The aim is to introduce classical statistical concepts and methods with emphasis on

methods used in epidemiology and public health. Learning outcomes : After successfully completing this course students should be able to: define the concept of

probability, laws of probability, and make simple probability calculations. suggest a statistical distribution todescribe a naturally occurring phenomenon and evaluate the appropriateness of the distribution given real data. present appropriate descriptive statistics for an epidemiological study. explain the difference between hypothesistesting and interval estimation and the relation between pvalues and confidence intervals. suggest anappropriate statistical test for a comparison of two groups, perform the hypothesis test using standard statisticalsoftware, and interpret the results. estimate and interpret three alternative measures of association betweenbinary exposures and binary outcomes and discuss the relative merits of each measure for a given researchquestion. explain the concept of confounding in epidemiological studies and demonstrate how to control/adjustfor confounding using stratified analysis. explain the basis of the linear regression model, fit a linear regressionmodel using standard statistical software, assess the fit of the model, and interpret the results.

Contents of the course : The course introduces classical statistical concepts and methods with emphasis onmethods used in epidemiology and public health. Topics covered include: the importance of statistical thinking;types of data (nominal, binary, discrete and continuous variables); data summary measures; contingency tables;graphical representations; notions of probability; probability models (distributions); principles of statisticalinference; parameter estimation (mean, proportion (prevalence), incidence and ratios); concepts of confidenceintervals and hypothesis tests; and a general introduction to correlation and linear regression models.

Teaching and learning activities : Lectures, exercises focusing on analysis of real data using statistical software,exercises not requiring statistical software, group discussions, literature review.

Examination : The course grade is based on the two written examinations. The course is divided into two parts,and each part will be examined separately. To pass the course, the student must pass both parts. Students who failwill be offered a reexamination within two months of the final day of the course. Students who fail the reexam willbe given top priority for admission the next time the course is offered. If the course is not offered during thefollowing two academic terms then another reexamination will be scheduled within 12 months of the final day ofthe course.

Compulsory elements : The individual written examinations (summative assessments) are compulsory. Number of students : 8 25

Selection of students : Eligible doctoral students will be prioritized according to 1) the relevance of the coursesyllabus for the applicant's doctoral project (according to written motivation), 2) date for registration as a doctoralstudent (priority given to earlier registration date). Give all information requested, including a short description ofcurrent research training and motivation for attending, as well as an account of previous courses taken. Priorknowledge in Stata software is strongly recommended.

More information : The course is extended over time in order to promote reflection and reinforce learning. Thecourse will be held the dates April 4, 5, 6, 9 and 10 (week 1) and April 18, 19, 20, 23 and 24 (week 2). Theindividual examination will be performed as an inclass examination the last course day of each week.

Course responsible : Matteo Bottai

The institute of Environmental Medicine 08524 870 24

[email protected]


[email protected]

Nobels väg 13

17177

Stockholm

Title : Biostatistics II: Logistic regression for epidemiologists




Specific entry requirements : Knowledge in epidemiology and biostatistics equivalent to "Epidemiology I:Introduction to epidemiology" and "Biostatistics I: Introduction for epidemiologists" or corresponding courses

Purpose of the course : This course focuses on the application of linear and logistic regression in the analysis ofepidemiological studies.

Learning outcomes : After successfully completing this course you as a student are expected to be able to: choose a suitable regression model for assessing a specific research hypothesis using data collected from anepidemiological study, fit the model using standard statistical software, evaluate the fit of the model, and interpretthe results. explain the concept of confounding in epidemiological studies and demonstrate how to control/adjustfor confounding using statistical models. apply and interpret appropriate statistical models for studying effectmodification. critically evaluate the methodological aspects (design and analysis) of a scientific article reporting anepidemiological study.

Contents of the course : This course focuses on the application of linear and logistic regression in the analysis ofepidemiological studies. Topics covered include a brief introduction to models for continuous data and a morecomplete coverage of binary outcome data, univariable and multivariable models, interpretation of parameters forcontinuous and categorical predictors, flexible modeling of quantitative predictors, confounding and interaction,model fitting and model diagnostics.

Teaching and learning activities : Lectures, computer lab with exercises focusing on analysis of real data setsusing statistical software, exercises not requiring statistical software, group discussions, literature review.

Examination : To pass the course, the student has to show that the learning outcomes have been achieved. Thecourse grade is based on the individual written examination (summative assessment). The focus of the examinationwill be on understanding concepts and their application to analysis of epidemiological studies rather thanmathematical detail. Students who do not obtain a passing grade in the first examination will be offered a secondexamination within two months of the final day of the course. Students who do not obtain a passing grade at thefirst two examinations will be given top priority for admission the next time the course is offered. If the course isnot offered during the following two academic terms then a third examination will be scheduled within 12 months ofthe final day of the course.

Compulsory elements : The individual written examination (summative assessment). Number of students : 8 25

Selection of students : Eligible doctoral students will be prioritized according to 1) the relevance of the coursesyllabus for the applicant's doctoral project (according to written motivation), 2) date for registration as a doctoralstudent (priority given to earlier registration date). Submit a completed application form. Give all informationrequested, including a short description of current research training and motivation for attending, and an account ofprevious courses taken.

More information : Course dates are: January 24, 25, 26, 29, 30 and 31. The course is extended over 2 weeks(but still 6 full course days) in order to promote reflection and reinforce learning. The individual examination will beperformed as a takehome examination. Prerequisite knowledge in epidemiology and biostatistics equivalent to"Epidemiology I:Introduction to epidemiology" and "Biostatistics I: Introduction for epidemiologists" orcorresponding courses. Prior knowledge in Stata software is strongly recommended.

Course responsible : Rino Bellocco


[email protected]

.



Title : Basic bioinformatics




Specific entry requirements : Basic knowledge in molecular biology from undergraduate level. Purpose of the course : The purpose of this course is to equip the students that work mainly in wet lab, with

several bioinformatic tools commonly used in molecular biology and genetics. Learning outcomes : By the end of the course the participants should be able to: use the command line

interface (a textbased means of interacting with a computer), download from omics databases know how toapply the basic principles for analyzing highthroughput sequencing data analysis and genomewide associationstudies. know how to perform logistic, linear regression and clustering analysis in python. have the foundationsto perform by themselves the taught data analysis techniques.

Contents of the course : Highthroughput sequencing data analysis (RNAseq, ChIPseq and rare variantdiscovery), genomewide association studies, genome browsers, plotting methods, logistic, linear regression andclustering in python.

Teaching and learning activities : The course consists primarily of handson computer exercises, and a limitednumber of lectures.

Examination : An individual project consisting of a practical exercise and a final seminar discussing each other'sprojects in small groups in line with the intended learning outcomes of the course.

Compulsory elements : Practical sessions are compulsory, unless stated they are not. Absence hasto be compensated for in agreement with the course organizer. The examination is compulsory.

Number of students : 10 25 Selection of students : Wet lab students without prior bioinformatics experience are given priority, and

secondarily date for registration as a doctoral student (priority given to earlier registration date). More information :

Course responsible : Daniel Ramsköld


[email protected]

Contact person : Lina DiazGallo

Institutionen för medicin, Solna +46851770310

[email protected]

Karolinska University Hospital CMM L8:05 DiazGallo

171 76 Stockholm

Title : Computational modelling and data analysis for cognitiveneuroscience




Specific entry requirements : Background in medicine, biomedicine, biology, psychology, cognitive science,medical imaging, computational biology or similar.

Purpose of the course : The purpose of the course is to introduce doctoral students to computational techniquesfor modelling and analysing cognitive neuroscience data, giving them practical experience applying these tools sothat they acquire enough understanding to enable them to 1) critically interpret the results of the studies in thefield and 2) adapt them to new experimental paradigms for their own research.

Learning outcomes : After successful course completion, the students will be able to independently use softwarepackages to analyse behavioural data from cognitive neuroscience experiments.

Contents of the course : The course will cover both theorydriven computational modelling and datadrivenanalysis approaches. Theorydriven approaches: Bayesian modelling; introduction to reinforcement learning;classical models for decisionmaking tasks (drift diffusion model, intertemporal choice). Datadriven approaches:supervised and unsupervised models in machine learning; classification and regression; dimensionality reduction;validation.

Teaching and learning activities : Lectures. Handson sessions with practical exercises. Examination : Examination consists of a practical assignment where students will model and analyse behavioural

data from a cognitive neuroscience experiment. The results will be reported and presented in front of the otherstudents in the last session.

Compulsory elements : Attending the lectures and handson sessions is mandatory. Absence from a lecture maybe compensated by writing an essay on the corresponding topic. The final examination (both presentation andassignment) is compulsory.



More information : The course dates are: 9th, 16th, 18th, 23rd and 25th of May 2018, from 9:00 to 16:00. Previous experience with statistical analysis and R, python or a similar language are desirable.

Course responsible : Benjamin Garzon

Department of Neurobiology, Care Sciences and Society

[email protected]

Contact person : Benjamin Garzon

Institutionen för neurobiologi, vårdvetenskap och samhälle

[email protected]

Rita Almeida Institutionen för neurovetenskap

[email protected]

Title : Causal inference: emulating a target trial to assesscomparative effectiveness




Specific entry requirements : Courses "Epidemiology I: Introduction to epidemiology", "Epidemiology II: Designof epidemiological studies", "Biostatistics I: Introduction for epidemiologists", "Biostatistics II: Logistic regressionfor epidemiologists", and either "Causal inference for epidemiological research" (course 2416) or "Causal Inferencefrom observational data" (course 2462) or corresponding courses.

Purpose of the course : This course focuses on a general framework for the assessment of comparativeeffectiveness and safety research, which can be applied to both observational data and randomized trials.

Learning outcomes : After successful completion of this course, the student should be able to: Formulatesufficiently welldefined causal questions for comparative effectiveness research Specify the protocol of the targettrial Design analyses of observational data that emulate the protocol of the target trial Identify key assumptionsfor a correct emulation of the target trial Decide when gmethods are required for data analysis Critiqueobservational studies and randomized trials for comparative effectiveness research

Contents of the course : The course introduces students to a general framework for the assessment ofcomparative effectiveness and safety research. The framework, which can be applied to both observational dataand randomized trials with imperfect adherence to the protocol, relies on the specification of a (hypothetical) targettrial. The course explores key challenges for comparative effectiveness research and critically reviews methodsproposed to overcome those challenges. The methods are presented in the context of several case studies forcancer, cardiovascular, renal, and infectious diseases.

Teaching and learning activities : Lectures and group sessions. Before the course, the student is required tostudy the course literature.

Examination : A written individual examination will be carried out after the course. The examination will requirethe evaluation of a published article on comparative effectiveness or safety. Students who do not obtain a passinggrade in the first examination will be offered a second examination within two months of the final day of the course. Compulsory elements : The individual written examination (summative assessment).

Number of students : 8 25 Selection of students : Eligible doctoral students, with required prerequisite knowledge, prioritized according to

1) the relevance of the course syllabus for the applicant's doctoral project (according to written motivation), 2) datefor registration as a doctoral student (priority given to earlier registration date). To be considered, submit acompleted application form. Give all information requested, including a description of current research andmotivation for attending, and an account of previous courses taken.

More information : Precourse reading is required: Chapters 13 of the book: Hernán MA, Robins JM(2017).Hernán MA, Robins JM (2017). Causal Inference. Boca Raton: Chapman & Hall/CRC, forthcoming. The bookcan be downloaded (for free) from http://www.hsph.harvard.edu/miguelhernan/causalinferencebook/. Theindividual examination will be performed as a takehome examination.

Course responsible : Anita Berglund


[email protected]


[email protected]

Nobels väg 13

17177

Stockholm

Title : Understanding and fighting disease using structural biology




Specific entry requirements : The course will be limited to 1214 participants decided by the course responsiblepersons

Purpose of the course : The course will first introduce Xray crystallography, electron microscopy (EM) andnuclear magnetic resonance spectroscopy (NMR), the three main methodologies used to experimentally determinethe threedimensional structure of proteins. Doctoral candidates will then be introduced to molecular dynamics(MD) simulations, analyze how point mutations can cause diseases at the molecular level and gain a basicunderstanding of the structurebased drug design process.

Learning outcomes : By following this course, doctoral candidates will learn how the threedimensional structureof proteins is determined, and how this information can be used to both understand human disease at themolecular level and facilitate the rational development of novel therapeutics. In particular, Ph.D. candidates will beable to understand the most important biochemical and biophysical properties of proteins and, based on thisknowledge, learn to choose and apply protocols for expressing and purifying proteins for structural studies.Following the practicals, the candidates will also be able to bioinformatically analyze protein sequences andstructures in order to predict their characteristics and functions. At the end of the Xray crystallography module,Ph.D. candidates will be able to read a protein crystallization diagram; list the different crystallization techniques;understand diffraction basics; describe the data collection, processing and refinement procedures; explain thephase problem and its solution by experimental phasing or molecular replacement; validate crystal structuresdownloaded from the Protein Data Bank. The electron microscopy module of the course will provide an introductionto the basics of EM. This knowledge will provide a foundation for understanding the technique and its applications.At the end of the module, the candidates will be able to understand the basics concepts of EM and its differencesfrom other structure determination techniques; list the advantages and limitations of EM for structuredetermination; describe the overall functioning and instrumentation of an electron microscope; explain theinteraction of electrons with the sample and the process of image formation; understand the principles of 3Dreconstruction from projection images; compare the process of model building in EM with other structuredetermination techniques. The NMR lecture will provide a basic overview of the information that one can obtain byspectroscopically probing the chemical environment of atomic nuclei. Doctoral candidates will understand how anNMR machine is built, what chemical shifts are, and what are the differences between 1D, 2D and 3D NMRexperiments. They will then be introduced to the concept of assignments, and how this can be combined with MDsimulations to produce a set of molecular models consistent with distance restraints derived from experimentalmeasurements. Towards this goal, an introduction to MD simulations will be given. Finally, the differences betweenNMRderived models and those obtained by the other techniques will be discussed. Thus, at the end of the lecture,the PhD candidates will be able to list the advantages and limitations of all methods presented and compare proteinstructures obtained through these different approaches. After the last lecture, the doctoral candidates will be ableto give recent examples describing how human mutations can cause diseases by affecting the structure of proteinsand their ability to perform their biological function. They will also have gained a basic knowledge of how leadcompounds/drugs bind to their molecular targets, and how structural biology can be of high medical relevance byallowing to optimize the affinity and specificity of this interaction.

Contents of the course : Theoretical: The lectures will open with an introduction to protein structure and function(1), followed by a presentation of protein expression and purification strategies (2). Then the theoreticalbackground needed for understanding Xray crystallography (3), EM (4) and NMR as well as MD simulations (5) willbe given. At the end, we will go through examples of how gene mutations can lead to diseases and explain howknowledge of molecular structures can contribute to drug discovery (6). Practical: The Ph.D. candidates will workthrough six projects during the two weeks: (1) analysis of protein structure elements and properties using PyMOL;(2) protein purification; (3) protein structure determination by Xray crystallography; (4) protein structuredetermination by EM; (5) comparison of protein structures obtained by Xray crystallography, EM and NMR usingPyMOL; (6) analysis of structurefunction relationship for a selection of medically relevant proteins.

Teaching and learning activities : Lectures, laboratory work, presentation and discussion of current biomedicallyrelevant research in the field of structural biology.

Examination : Reports from practical exercises and journal clublike presentations of scientific articles describingprotein structure of biomedical interest. ILOs will be studied both theoretically and through practical exercises.Each ILO will be tested through questionnaires that have to be submitted in electronic form at the end of each day.

Compulsory elements : Seminar presentations and laboratory work are compulsory. If a Ph.D. candidate misses apractical exercise, they will be given a chance to complete it at another occasion set by the organizers.



More information : The course is given jointly by the doctoral programmes in Neuroscience, Development andregeneration, Metabolism and endocrinology and Tumor Biology and Oncology. See: http://ki.se/en/staff/doctoral

programmes.

Course responsible : Hans Hebert

Department of Biosciences and Nutrition

[email protected]

Contact person : Luca Jovine

Institutionen för biovetenskaper och näringslära

[email protected]

Carsten Mim Institutionen för biovetenskaper och näringslära

[email protected]

Title : Cellular Signalling



Level : Doctoral level Responsible KI department : Department for Clinical Science, Intervention and Technology

Specific entry requirements : Purpose of the course : The purpose of the course is to give a broad view of various signalling pathways and

enable to identify common themes on proteinprotein and proteinlipid interactions. The students shall learn on howsignal transduction occurs through a highly regulated cascade of events in side cells. The student should identifyand reflect the knowledge (general methodology and theoretical concepts) gained with the benefit for ownresearch.

Learning outcomes : After the course, the student: should be able to show adaquate knowledge on currentcommon methods and techniques, in the field of signal transduction. should be able to hold a journal clubpresentation in the field of signal transduction. should be able to apply some of the conceptual knowledge inhis/her own research project(s).

Contents of the course : The course brings up current aspects in cellular signalling and the developments inunderstanding the function of the different signalling pathways in various cell model systems. The course will covermajor aspects of protein and lipid kinases, heterotrimeric Gproteins, small GTPases, cytokine and growth hormonereceptors, secondary messengers, transcriptional regulation and signal transduction in cell specific responses tostimuli. In the context of the functional genomic era, the course will cover the molecular basis of certain diseasesrelated to the abrogation of signalling pathways.

Teaching and learning activities : Lectures, presentations and individual discussions with all participants.Students are encouraged to take up additional new topics with the course leader and lecturers. Discussions aboutresources to retrieve additional information about a particular issue within the field of signal transduction.

Examination : Oral Presentation is compulsory and it is essential to be an active participants in the discussions. Ithas to be shown that all the intended learning outcomes of the course are achieved.

Compulsory elements : All lectures and activity moments are compulsory, missing lectures must be compensatedby written résumé, while activity moments should be taken again in the next course occasion.



More information : Time: Monday to Friday, 9:00 16:00; Location: Novum, Karolinska Institutet CampusFlemingsberg. The evaluation report below is from the same course last year, but with a different course number.

Course responsible : Anna Witasp

Department for Clinical Science, Intervention and Technology

[email protected]

Contact person : Anna Witasp


[email protected]

Course catalogue for doctoral education VT18kiwas.ki.se/kicoursecatalogueVT18.pdf · 2641 Sickness...

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